The Structure of Sedoheptulose-7-Phosphate Isomerase from Burkholderia pseudomallei Reveals a Zinc Binding Site at the Heart of the Active Site

Journal of Molecular Biology

Volumn 400, Issue 3, 2010, Pages 379-392

  Harmer, Nicholas J ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Burkholderia pseudomallei; Capsule biosynthesis; GmhA; Isomerase; Zinc binding

Indexed keywords

BACTERIAL ENZYME; SEDOHEPTULOSE 7 PHOSPHATE ISOMERASE; UNCLASSIFIED DRUG; ZINC ION;

ARTICLE; BINDING SITE; BURKHOLDERIA PSEUDOMALLEI; CATALYSIS; ENZYME ACTIVITY; PRIORITY JOURNAL;

BURKHOLDERIA PSEUDOMALLEI;

EID: 77954387276     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.04.058     Document Type: Article

References (44)

1. Hsueh P.-R., Teng L.-J., Lee L.-N., Yu C.-J., Yang P.-C., Ho S.-W., Luh K.-T. Melioidosis: an emerging infection in Taiwan?. Emerg. Infect. Dis. 2001, 7:428-433.
2. Stone R. Racing to defuse a bacterial time bomb. Science 2007, 317:1021-1023.
3. Wiersinga W.J., van der Poll T., White N.J., Day N.P., Peacock S.J. Melioidosis: insights into the pathogenicity of Burkholderia pseudomallei. Nat. Rev., Microbiol. 2006, 4:272-282.
4. White N. Melioidosis. Lancet 2003, 361:1715-1722.
5. John T., Jesudason M., Lalitha M., Ganesh A., Mohandas V., Cherian T., et al. Melioidosis in India: the tip of the iceberg. Indian J. Med. Res. 1996, 103:62-65.
6. Lazar Adler N.R., Govan B., Cullinane M., Harper M., Adler B., Boyce J.D. The molecular and cellular basis of pathogenesis in melioidosis: how does Burkholderia pseudomallei cause disease?. FEMS Microbiol. Rev. 2009, 33:1079-1099.
7. Jenney A.W., Lum G., Fisher D.A., Currie B.J. Antibiotic susceptibility of Burkholderia pseudomallei from tropical northern Australia and implications for therapy of melioidosis. Int. J. Antimicrob. Agents 2001, 17:109-113.
8. Ngauy V., Lemeshev Y., Sadkowski L., Crawford G. Cutaneous melioidosis in a man who was taken as a prisoner of war by the Japanese during World War II. J. Clin. Microbiol. 2005, 43:970-972.
9. Rotz L.D., Khan A.S., Lillibridge S.R., Ostroff S.M., Hughes J.M. Public health assessment of potential biological terror agents. Emerg. Infect. Dis. 2002, 8:225-230.
10. Valvano M.A., Messner P., Kosma P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 2002, 148:1979-1989.
11. Caroff M., Karibian D. Structure of bacterial lipopolysaccharides. Carbohydr. Res. 2003, 338:2431-2447.
12. Raetz C., Reynolds C., Trent M., Bishop R. Lipid A modification systems in Gram-negative bacteria. Ann. Rev. Biochem. 2007, 76:295-329.
13. Whitfield C. Biosynthesis and assembly of capsular polysaccharides in Escherichia coli. Ann. Rev. Biochem. 2006, 75:39-68.
14. Reckseidler S.L., DeShazer D., Sokol P.A., Woods D.E. Detection of bacterial virulence genes by subtractive hybridization: identification of capsular polysaccharide of Burkholderia pseudomallei as a major virulence determinant. Infect. Immun. 2001, 69:34-44.
15. Atkins T., Prior R., Mack K., Russell P., Nelson M., Prior J., et al. Characterisation of an acapsular mutant of Burkholderia pseudomallei identified by signature tagged mutagenesis. J. Med. Microbiol. 2002, 51:539-547.
16. Nelson M., Prior J., Lever M.S., Jones H.E., Atkins T.P., Titball R.W. Evaluation of lipopolysaccharide and capsular polysaccharide as subunit vaccines against experimental melioidosis. J. Med. Microbiol. 2004, 53:1177-1182.
17. Cuccui J., Easton A., Chu K., Bancroft G., Oyston P., Titball R., Wren B. Development of signature-tagged mutagenesis in Burkholderia pseudomallei to identify genes important in survival and pathogenesis. Infect. Immun. 2007, 75:1186-1195.
18. Warawa J., Long D., Rosenke R., Gardner D., Gherardini C. A role for the Burkholderia pseudomallei capsular polysaccharide encoded by the wcb operon in acute disseminated melioidosis. Infect. Immun. 2009, 77:5252-5261.
19. Reckseidler-Zenteno S.L., DeVinney R., Woods D.E. The capsular polysaccharide of Burkholderia pseudomallei contributes to survival in serum by reducing complement factor C3b deposition. Infect. Immun. 2005, 73:1106-1115.
20. DeShazer D., Waag D.M., Fritz D.L., Woods D.E. Identification of a Burkholderia mallei polysaccharide gene cluster by subtractive hybridization and demonstration that the encoded capsule is an essential virulence determinant. Microb. Pathog. 2001, 30:253-269.
21. Pacinelli E., Wang L., Reeves P.R. Relationship of Yersinia pseudotuberculosis O antigens IA, IIA, and IVB: the IIA gene cluster was derived from that of IVB. Infect. Immun. 2002, 70:3271-3276.
22. St.Michael F., Szymanski C., Li J., Chan K., Khieu N., Larocque S., et al. The structures of the lipooligosaccharide and capsule polysaccharide of Campylobacter jejuni genome sequenced strain NCTC 11168. Eur. J. Biochem. 2002, 269:5119-5136.
23. Butty F., Aucoin M., Morrison L., Ho N., Shaw G., Creuzenet C. Elucidating the formation of 6-deoxyheptose: biochemical characterisation of the GDP-d-glycero-d-manno-heptose C6 dehydratase, DmhA, and its associated C4 reductase, DmhB. Biochemistry 2009, 48:7764-7775.
24. Taylor P.L., Wright G.D. Novel approaches to discovery of antibacterial agents. Anim. Health Res. Rev. 2008, 9:237-246.
25. Seetharaman J., Kanagalaghatta R.R., Solorzano V., Kniewel R., Lima C.D., Bonanno J.B., et al. Crystal structures of two putative phosphoheptose isomerases. Proteins: Struct. Funct. Bioinf. 2006, 63:1092-1096.
26. Taylor P.L., Blakely K.M., De Leon G.P., Walker J.R., McArthur F., Evdokimova E., et al. Structure and function of GmhA (sedoheptulose 7-phopshate isomerase): a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants. J. Biol. Chem. 2008, 283:2835-2845.
27. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
28. Mizuguchi K., Deane C.M., Blundell T., Johnson M.S., Overington J.P. JOY: protein sequence-structure representation and analysis. Bioinformatics 1998, 14:617-623.
29. Overington J., Johnson M.S., Sali A., Blundell T. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc. R. Soc. London, Ser. B 1990, 241:132-145.
30. Sheldrick G.M. A short history of SHELX. Acta Crystallogr., Sect. A: Found. Crystallogr. 2008, 64:112-122.
31. Holliday G.L., Almonacid D.E., Bartlett G.J., O'Boyle N.M., Torrance J.W., Murray-Rust P., et al. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res. 2007, 35:D515-D520.
32. Cameron A.D., Ridderström M., Olin B., Kavarana M.J., Creighton D.J., Mannervik B. Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue. Biochemistry 1999, 38:13480-13490.
33. Studier F.W. Protein production by auto-induction in high-density shaking cultures. Protein Expression Purif. 2005, 41:207-234.
34. Leslie A. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 ESF-EAMCB Newslett. Protein Crystallogr. 1992, 26.
35. Evans P.R. Scaling and assessment of data quality. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, 62:72-82.
36. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 2007, 40:658-674.
37. Pape T., Schneider T.R. HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Crystallogr. 2004, 37:843-844.
38. Vonrhein C., Blanc E., Roversi P., Bricogne G. Automated structure solution with autoSHARP. Methods Mol. Biol. 2008, 364:215-230.
39. Langer G., Cohen S.X., Lamzin V.S., Perrakis A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 2008, 3:1171-1179.
40. Emsley P., Lohkamp B., Scott W.G., Cowtan K. Features and development of Coot. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66:486-501.
41. Adams P.D., Grosse-Kunstleve R.W., Hung L.-W., Ioerger T.R., McCoy A.J., Moriarty N.W., et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58:1948-1954.
42. Painter J., Merritt E.A. TLSMD web server for the generation of multi-group TLS models. J. Appl. Crystallogr. 2006, 39:109-111.
43. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., Wang X., et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007, 35:W375-W383.
44. De Leon G.P., Elowe N.H., Koteva K.P., Valvano M.A., Wright G.D. An in vitro screen of bacterial lipopolysaccharide biosynthetic enzymes identifies an inhibitor of ADP-heptose biosynthesis. Chem. Biol. 2006, 13:437-441.