Novel purified polypeptides from bacteria

• US 20050181464A1
• Filed: 09/29/2004
• Published: 08/18/2005
• Est. Priority Date: 04/04/2002
• Status: Abandoned Application

• Current Assignee: Affinium Pharmaceuticals, Inc.
• Original Assignee: Affinium Pharmaceuticals, Inc.
• Inventors: Li, Qin, Ouyang, Hui, Richards, Dawn, Virag, Cristina, Buzadzija, Kristina, Nethery-Brokx, Kathleen, McDonald, Merry-Lynn, Mansoury, Kamran, Kanagarajah, Dhushy, Edwards, Aled, Awrey, Donald E., Clarke, Teresa, Beattie, Bryan, Vedadi, Masoud, Domagala, Megan, Arrowsmith, Cheryl, Dharamsi, Akil, Vallee, Francois, Alam, Muhammad Zahoor, Ng, Ivy, Houston, Simon
• Application Number:
  US10/953,901
• Publication Number:
  US 20050181464A1
• Time in Patent Office: Days
• US Class Current: 435/7.320
• CPC Class Codes: B01D 15/3804 Affinity chromatography
• CPC Class Codes: C07K 14/205 from Campylobacter (G)
• CPC Class Codes: C07K 14/21 from Pseudomonadaceae (F)
• CPC Class Codes: C07K 14/245 Escherichia (G)
• CPC Class Codes: C07K 14/31 from Staphylococcus (G)
• CPC Class Codes: C07K 14/315 from Streptococcus (G), e.g. Enterococci
• CPC Class Codes: C07K 14/3156 from Streptococcus pneumoniae (Pneumococcus) Streptokinase C07K14/3153
• CPC Class Codes: C12N 1/06 Lysis of microorganisms
• CPC Class Codes: C12N 9/0006 acting on CH-OH groups as donors (1.1)
• CPC Class Codes: C12N 9/0008 acting on the aldehyde or oxo group of donors (1.2)
• CPC Class Codes: C12N 9/0016 with NAD or NADP as acceptor (1.4.1)
• CPC Class Codes: C12N 9/1022 transferring aldehyde or ketonic groups (2.2)
• CPC Class Codes: C12N 9/1029 transferring groups other than amino-acyl groups (2.3.1)
• CPC Class Codes: C12N 9/1205 Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
• CPC Class Codes: C12N 9/1247 DNA-directed RNA polymerase (2.7.7.6)
• CPC Class Codes: C12N 9/1252 DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
• CPC Class Codes: C12N 9/1288 Transferases for other substituted phosphate groups (2.7.8)
• CPC Class Codes: C12N 9/48 acting on peptide bonds (3.4)
• CPC Class Codes: C12N 9/78 acting on carbon to nitrogen bonds other than peptide bonds (3.5)
• CPC Class Codes: C12N 9/88 Lyases (4.)
• CPC Class Codes: C12N 9/90 : Isomerases (5.)
• CPC Class Codes: C12N 9/93 : Ligases (6)

Abstract

The present invention relates to polypeptide targets for pathogenic bacteria. The invention also provides biochemical and biophysical characteristics of those polypeptides.

Claims

1. A composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises:

(a) an amino acid sequence set forth in SEQ ID NO;

563 or SEQ ID NO;

565;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

563 or SEQ ID NO;

565;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

562 or SEQ ID NO;

564 and has at least one biological activity of enoyl-(acyl-carrier-protein) reductase (NADH) from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition.

2. The composition of claim 1, wherein at least about two-thirds of the polypeptide in the sample is soluble.

3. The composition of claim 1, wherein the polypeptide is fused to at least one heterologous polypeptide that increases the solubility or stability of the polypeptide.

4. The composition of claim 1, further comprising a matrix suitable for mass spectrometry.

5. The composition of claim 1, wherein the matrix is a nicotinic acid derivative or a cinnamic acid derivative.

6. A composition of claim 1, wherein the polypeptide is enriched in at least one NMR isotope.

7. The composition of claim 6, wherein the NMR isotope is one of the following:

hydrogen-1 (1 H), hydrogen-2 (2H), hydrogen-3 (3H), phosphorous-31 (3 1P), sodium-23 (23Na), nitrogen-14 (14N), nitrogen-15 (15N), carbon-13 (13C) and fluorine-19 (19F).

8. The composition of claim 6, further comprising a deuterium lock solvent.

9. The composition of claim 8, wherein the deuterium lock solvent is one of the following:

acetone (CD3COCD3), chloroform (CDC13), dichloromethane (CD2Cl2), methylnitrile (CD3CN), benzene (C6D6), water (D2O), diethylether ((CD3CD2)2O), dimethylether ((CD3)2O), N,N-dimethylformamide ((CD3)2NCDO), dimethyl sulfoxide (CD3SOCD3), ethanol (CD3CD2OD), methanol (CD3OD), tetrahydrofuran (C4D8O), toluene (C6D5CD3), pyridine (C5D5N) and cyclohexane (C6H12).

10. The composition of claim 1, wherein the polypeptide is labeled with a heavy atom.

11. The composition of claim 10, wherein the heavy atom is one of the following:

cobalt, selenium, krypton, bromine, strontium, molybdenum, ruthenium, rhodium, palladium, silver, cadmium, tin, iodine, xenon, barium, lanthanum, cerium, praseodymium, neodymium, samarium, europium, gadolinium, terbium, dysprosium, holmium, erbium, thulium, ytterbium, lutetium, tantalum, tungsten, rhenium, osmium, iridium, platinum, gold, mercury, thallium, lead, thorium and uranium.

12. The composition of claim 10, wherein the polypeptide is labeled with seleno-methionine.

21. A host cell comprising a nucleic acid encoding a polypeptide of claim 1;

wherein a culture of the host cell produces at least about 1 mg of the polypeptide per liter of culture and the polypeptide is at least about one-third soluble as measured by gel electrophoresis.

85. A composition selected from the group consisting of:

A) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

5 or SEQ ID NO;

7;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

5 or SEQ ID NO;

7;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

4 or SEQ ID NO;

6 and has at least one biological activity of lysyl-tRNA synthetase from S. aureus;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

B) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

14 or SEQ ID NO;

16;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

14 or SEQ ID NO;

16;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

13 or SEQ ID NO;

15 and has at least one biological activity of valine tRNA synthetase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

C) a composition comprising an isolated, recombinant polypeptide comprising;

(a) an amino acid sequence set forth in SEQ ID NO;

23 or SEQ ID NO;

25;

(b) an amino acid sequence having at least about 90% identity with the amino acid sequence set forth in SEQ ID NO;

23 or SEQ ID NO;

25;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

22 or SEQ ID NO;

24 and has at least one biological activity of aspartate tRNA synthetase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

D) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

32 or SEQ ID NO;

34;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

32 or SEQ ID NO;

34;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

31 or SEQ ID NO;

33 and has at least one biological activity of cysteine tRNA synthetase from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

E) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

41 or SEQ ID NO;

43;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

41 or SEQ ID NO;

43;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

40 or SEQ ID NO;

42 and has at least one biological activity of malonyl-CoA-[acyl-carrier-protein] transacylase from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

F) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

50 or SEQ ID NO;

52;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

50 or SEQ ID NO;

52;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

49 or SEQ ID NO;

51 and has at least one biological activity of glutamate tRNA synthetase, catalytic subunit from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

G) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

59 or SEQ ID NO;

61;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

59 or SEQ ID NO;

61;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

58 or SEQ ID NO;

60 and has at least one biological activity of protein chain initiation factor IF-1 from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

H) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

68 or SEQ ID NO;

70;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

68 or SEQ ID NO;

70;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

67 or SEQ ID NO;

69 and has at least one biological activity of translation initiation factor IF-3 from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

I) A composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

77 or SEQ ID NO;

79;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

77 or SEQ ID NO;

79;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

76 or SEQ ID NO;

78 and has at least one biological activity of threonine tRNA synthetase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

J) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

86 or SEQ ID NO;

88;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

86 or SEQ ID NO;

88;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

85 or SEQ ID NO;

87 and has at least one biological activity of conserved hypothetical protein from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

K) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

95 or SEQ ID NO;

97;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

95 or SEQ ID NO;

97;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

94 or SEQ ID NO;

96 and has at least one biological activity of cysteine tRNA synthetase from E. coli; and

wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

L) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

104 or SEQ ID NO;

106;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

104 or SEQ ID NO;

106;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

103 or SEQ ID NO;

105 and has at least one biological activity of DNA polymerase III, beta-subunit from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

M) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

113 or SEQ ID NO;

115;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

113 or SEQ ID NO;

115;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

112 or SEQ ID NO;

114 and has at least one biological activity of 3-oxoacyl-[acyl-carrier-protein] synthase II from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

N) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

122 or SEQ ID NO;

124;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

122 or SEQ ID NO;

124;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

121 or SEQ ID NO;

123 and has at least one biological activity of methionine aminopeptidase from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

O) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

131 or SEQ ID NO;

133;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

131 or SEQ ID NO;

133;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

130 or SEQ ID NO;

132 and has at least one biological activity of pyruvate kinase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

P) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

140 or SEQ ID NO;

142;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

140 or SEQ ID NO;

142;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

139 or SEQ ID NO;

141 and has at least one biological activity of threonine tRNA synthetase from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

Q) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in or;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

149 or SEQ ID NO;

151;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

148 or SEQ ID NO;

150 and has at least one biological activity of putative ATP-binding component of a transport system from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

R) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

158 or SEQ ID NO;

160;

(b) an amino acid sequence having at least about 95% identity with the anino acid sequence set forth in SEQ ID NO;

158 or SEQ ID NO;

160;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

157 or SEQ ID NO;

159 and has at least one biological activity of glucose-6-phosphate dehydrogenase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

S) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

167 or SEQ ID NO;

169;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

167 or SEQ ID NO;

169;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

166 or SEQ ID NO;

168 and has at least one biological activity of alanyl-tRNA synthetase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

T) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

176 or SEQ ID NO;

178;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

176 or SEQ ID NO;

178;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

175 or SEQ ID NO;

177 and has at least one biological activity of glutamate tRNA synthetase, catalytic subunit from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

U) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

185 or SEQ ID NO;

187;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

185 or SEQ ID NO;

187;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

184 or SEQ ID NO;

186 and has at least one biological activity of isoleucine tRNA synthetase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

V) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

194 or SEQ ID NO;

196;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

194 or SEQ ID NO;

196;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

193 or SEQ ID NO;

195 and has at least one biological activity of RNA polymerase beta-prime chain from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

W) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

203 or SEQ ID NO;

205;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

203 or SEQ ID NO;

205;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

202 or SEQ ID NO;

204 and has at least one biological activity of RNA polymerase sigma-70 factor from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

X) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

212 or SEQ ID NO;

214;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

212 or SEQ ID NO;

214;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

211 or SEQ ID NO;

213 and has at least one biological activity of transketolase 1 isozyme from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

Y) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

221 or SEQ ID NO;

223;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

221 or SEQ ID NO;

223;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

220 or SEQ ID NO;

222 and has at least one biological activity of tryptophan tRNA synthetase from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

Z) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

230 or SEQ ID NO;

232;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

230 or SEQ ID NO;

232;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

229 or SEQ ID NO;

231 and has at least one biological activity of holo-(acyl-carrier protein) synthase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

AA) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

239 or SEQ ID NO;

241;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

239 or SEQ ID NO;

241;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

238 or SEQ ID NO;

240 and has at least one biological activity of glutamate racemase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

BB) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

248 or SEQ ID NO;

250;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

248 or SEQ ID NO;

250;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

247 or SEQ ID NO;

249 and has at least one biological activity of glutamate racemase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

CC) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

257 or SEQ ID NO;

259;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

257 or SEQ ID NO;

259;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

256 or SEQ ID NO;

258 and has at least one biological activity of aspartate tRNA synthetaseC from S. pneumoniaeC;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

DD) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

266 or SEQ ID NO;

268;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

266 or SEQ ID NO;

268;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

265 or SEQ ID NO;

267 and has at least one biological activity of gamma-glutamyl phosphate reductase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

EE) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

275 or SEQ ID NO;

277;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

275 or SEQ ID NO;

277;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

274 or SEQ ID NO;

276 and has at least one biological activity of triosephosphate isomerase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

FF) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

284 or SEQ ID NO;

286;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

284 or SEQ ID NO;

286;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

283 or SEQ ID NO;

285 and has at least one biological activity of triosephosphate isomerase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

GG) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

293 or SEQ ID NO;

295;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

293 or SEQ ID NO;

295;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

292 or SEQ ID NO;

294 and has at least one biological activity of branched-chain alpha-keto acid dehydrogenase from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

HH) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

302 or SEQ ID NO;

304;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

302 or SEQ ID NO;

304;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

301 or SEQ ID NO;

303 and has at least one biological activity of tetrahydrodipicolinate (THDP) N-succinyltransferase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

II) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

311 or SEQ ID NO;

313;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

311 or SEQ ID NO;

313;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

310 or SEQ ID NO;

312 and has at least one biological activity of elongation factor P (EF-P) from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

JJ) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

320 or SEQ ID NO;

322;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

320 or SEQ ID NO;

322;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

319 or SEQ ID NO;

321 and has at least one biological activity of fructose-bisphosphate aldolase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

KK) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

329 or SEQ ID NO;

331;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

329 or SEQ ID NO;

331;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

328 or SEQ ID NO;

330 and has at least one biological activity of isopentenyl diphosphate isomerase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

LL) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

338 or SEQ ID NO;

340;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

338 or SEQ ID NO;

340;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

337 or SEQ ID NO;

339 and has at least one biological activity of glutamate dehydrogenase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

MM) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

347 or SEQ ID NO;

349;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

347 or SEQ ID NO;

349;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

346 or SEQ ID NO;

348 and has at least one biological activity of GroEL protein from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

NN) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

356 or SEQ ID NO;

358;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

356 or SEQ ID NO;

358;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

355 or SEQ ID NO;

357 and has at least one biological activity of ATP-binding component of molybdate transport system from S. aureus;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

OO) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

365 or SEQ ID NO;

367;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

365 or SEQ ID NO;

367;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

364 or SEQ ID NO;

366 and has at least one biological activity of DNA topoisomerase IV subunit A from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

PP) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

374 or SEQ ID NO;

376;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

374 or SEQ ID NO;

376;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

373 or SEQ ID NO;

375 and has at least one biological activity of GTP cyclohydrolase II from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

QQ) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

383 or SEQ ID NO;

385;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

383 or SEQ ID NO;

385;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

382 or SEQ ID NO;

384 and has at least one biological activity of putative aspartate-semialdehyde dehydrogenase from E. faecalis;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition.The composition of claim 1, wherein the polypeptide is purified to essential homogeneity;

RR) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

392 or SEQ ID NO;

394;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

392 or SEQ ID NO;

394;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

391 or SEQ ID NO;

393 and has at least one biological activity of elongation factor P (EF-P) from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

SS) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

401 or SEQ ID NO;

403;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

401 or SEQ ID NO;

403;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

400 or SEQ ID NO;

402 and has at least one biological activity of GroES protein from S. aureus;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

TT) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

410 or SEQ ID NO;

412;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

410 or SEQ ID NO;

412;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

409 or SEQ ID NO;

411 and has at least one biological activity of GroES protein from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

UU) a composition comprising an isolated, recombinant polypeptide comprising;

(a) an amino acid sequence set forth in SEQ ID NO;

419 or SEQ ID NO;

421;

(b) an amino acid sequence having at least about 90% identity with the amino acid sequence set forth in SEQ ID NO;

419 or SEQ ID NO;

421;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

418 or SEQ ID NO;

420 and has at least one biological activity of GroES protein from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

VV) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

428 or SEQ ID NO;

430;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

428 or SEQ ID NO;

430;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

427 or SEQ ID NO;

429 and has at least one biological activity of transcription termination factor NusG from E. coli; and

wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

WW) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

437 or SEQ ID NO;

439;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

437 or SEQ ID NO;

439;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

436 or SEQ ID NO;

438 and has at least one biological activity of GrpE protein from S. aureus;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

XX) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

446 or SEQ ID NO;

448;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

446 or SEQ ID NO;

448;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

445 or SEQ ID NO;

447 and has at least one biological activity of transcription termination factor NusG from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

YY) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

455 or SEQ ID NO;

457;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

455 or SEQ ID NO;

457;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

454 or SEQ ID NO;

456 and has at least one biological activity of transcription termination factor NusG from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

ZZ) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

464 or SEQ ID NO;

466;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

464 or SEQ ID NO;

466;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

463 or SEQ ID NO;

465 and has at least one biological activity of DNA-directed RNA polymerase, alpha subunit from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

AAA) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

473 or SEQ ID NO;

475;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

473 or SEQ ID NO;

475;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

472 or SEQ ID NO;

474 and has at least one biological activity of DNA-directed RNA polymerase, alpha subunit from S. aureus;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

BBB) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

482 or SEQ ID NO;

484;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

482 or SEQ ID NO;

484;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

481 or SEQ ID NO;

483 and has at least one biological activity of prolyl-tRNA synthetase from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

CCC) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

491 or SEQ ID NO;

493;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

491 or SEQ ID NO;

493;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

490 or SEQ ID NO;

492 and has at least one biological activity of seryl-tRNA synthetase from S. pneumoniae;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

DDD) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

500 or SEQ ID NO;

502;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

500 or SEQ ID NO;

502;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

499 or SEQ ID NO;

501 and has at least one biological activity of L-cysteine desulfurase from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

EEE) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

509 or SEQ ID NO;

511;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

509 or SEQ ID NO;

511;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

508 or SEQ ID NO;

510 and has at least one biological activity of RhlR and LasR homologue from E. coli; and

wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

FFF) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

518 or SEQ ID NO;

520;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

518 or SEQ ID NO;

520;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

517 or SEQ ID NO;

519 and has at least one biological activity of autoinducer synthesis protein RhlI from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

GGG) a composition comprising an isolated, recombinant polypeptide comprising;

(a) an amino acid sequence set forth in SEQ ID NO;

527 or SEQ ID NO;

529;

(b) an amino acid sequence having at least about 90% identity with the amino acid sequence set forth in SEQ ID NO;

527 or SEQ ID NO;

529;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

526 or SEQ ID NO;

528 and has at least one biological activity of autoinducer synthesis protein LasI from P. aeruginosa;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

HHH) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

536 or SEQ ID NO;

538;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

536 or SEQ ID NO;

538;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

535 or SEQ ID NO;

537 and has at least one biological activity of adenylate kinase from S. aureus;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

III) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

545 or SEQ ID NO;

547;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

545 or SEQ ID NO;

547;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

544 or SEQ ID NO;

546 and has at least one biological activity of UDP-N-acetylglucosamine pyrophosphorylase (glmU) from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

JJJ) a composition comprising an isolated, recombinant polypeptide comprising;

(a) an amino acid sequence set forth in SEQ ID NO;

554 or SEQ ID NO;

556;

(b) an amino acid sequence having at least about 90% identity with the amino acid sequence set forth in SEQ ID NO;

554 or SEQ ID NO;

556;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

553 or SEQ ID NO;

555 and has at least one biological activity of geranyltranstransferase (farnesyldiphosphate synthase) from E. coli; and

wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition;

KKK) a composition comprising an isolated, recombinant polypeptide, wherein the polypeptide comprises;

(a) an amino acid sequence set forth in SEQ ID NO;

572 or SEQ ID NO;

574;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

572 or SEQ ID NO;

574;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

571 or SEQ ID NO;

573 and has at least one biological activity of ribonucleoside diphosphate reductase, beta subunit from H. pylori;

and wherein the polypeptide of (a), (b) or (c) is at least about 90% pure in a sample of the composition.

13. A crystallized, recombinant polypeptide comprising:

(a) an amino acid sequence set forth in SEQ ID NO;

563 or SEQ ID NO;

565;

(b) an amino acid sequence having at least about 95% identity with the amino acid sequence set forth in SEQ ID NO;

563 or SEQ ID NO;

565;

or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO;

562 or SEQ ID NO;

564 and has at least one biological activity of enoyl-(acyl-carrier-protein) reductase (NADH) from H. pylori;

wherein the polypeptide of (a), (b) or (c) is in crystal form.

14. The crystallized, recombinant polypeptide of claim 13, wherein the polypeptide is labeled with a heavy atom.

15. The crystallized, recombinant polypeptide of claim 13, wherein the polypeptide is labeled with seleno-methionine.

16. The crystallized, recombinant polypeptide of claim 13, which diffracts x-rays to a resolution of about 3.5 Å

or better.

17. A crystallized complex comprising the crystallized, recombinant polypeptide of claim 13 and a co-factor, wherein the complex is in crystal form.

18. A crystallized complex comprising the crystallized, recombinant polypeptide of claim 13 and a small organic molecule, wherein the complex is in crystal form.

19. A composition comprising the crystallized, recombinant polypeptide of claim 13 and a cryo-protectant.

20. The composition of claim 19, wherein the cryo-protectant is one of the following:

methyl pentanediol, isopropanol, ethylene glycol, glycerol, formate, citrate, mineral oil and a low-molecular-weight polyethylene glycol.

22-84. -84. (canceled)