The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation

Journal of Structural and Functional Genomics

Volumn 10, Issue 3, 2009, Pages 209-217

  Weyand, Simone ^a,b,c   Kefala, Georgia ^a,d   Svergun, Dmitri I ^a   Weiss, Manfred S ^a  

^a DESY   (Germany)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c Diamond Light Source   (United Kingdom)

^d The Salk Institutes   (United States)

Author keywords

DAPDC; Diaminopimelate decarboxylase; LysA; Lysine biosynthesis; Mycobacterium tuberculosis; PLP binding protein; X ray crystallography

Indexed keywords

AMINOTRANSFERASE; BACTERIAL ENZYME; CARBOXYLYASE; DIAMINOPIMELATE DECARBOXYLASE; TETRAMER; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME STRUCTURE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; SOLUTION AND SOLUBILITY; X RAY CRYSTALLOGRAPHY;

BACTERIAL PROTEINS; BINDING SITES; CARBOXY-LYASES; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; LYSINE; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PROTEIN CONFORMATION;

MYCOBACTERIUM TUBERCULOSIS;

EID: 69949088958     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-009-9065-z     Document Type: Article

References (51)

1. WHO (2008) Global tuberculosis control: surveillance, planning, financing WHO, Geneva. http://www.who.int/tb/publications/global-report/en/index.html
2. D Smith E Wiegeshaus V Balasubramanian 2000 An analysis of some hypotheses related to the Chingelput bacille Calmette-Guerin trial Clin Infect Dis 31 S77 S80
3. J-C Camus MJ Pryor C Médigue ST Cole 2002 Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv Microbiology 148 2967 2973
4. ST Cole R Brosch J Parkhill T Garnier C Churcher D Harris SV Gordon K Eiglmeier S Gas CE Barry F Tekaia K Badcock D Basham D Brown T Chillingworth R Connor R Davies K Devlin T Feltwell S Gentles N Hamlin S Holroyd T Hornsby K Jagels A Krogh J McLean S Moule L Murphy K Oliver J Osborne MA Quail M-A Rajandream J Rogers S Rutter K Seeger J Skelton R Squares S Squares JE Sulston K Taylor S Whitehead BG Barrell 1998 Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Nature 393 537 544 (Erratum in: Nature 396:190, 1998)
5. RD Fleischmann D Alland JA Eisen L Carpenter O White J Peterson R DeBoy R Dodson M Gwinn D Haft E Hickey JF Kolonay WC Nelson LA Umayam M Ermolaeva SL Salzberg A Delcher T Utterback J Weidman H Khouri J Gill A Mikula W Bishai WR Jacobs Jr JC Venter CM Fraser 2002 Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains J Bacteriol 184 5479 5490
6. CA Hutton TJ Southwood JJ Turner 2003 Inhibitors of lysine biosynthesis as antibacterial agents Mini Rev Med Chem 3 115 127
7. K Gokulan B Rupp MS Pavelka Jr WR Jacobs Jr JC Sacchettini 2003 Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis J Biol Chem 278 18588 18596
8. C Momany V Levdikov L Blagova K Crews 2002 Crystallization of diaminopimelate decarboxylase from Escherichia coli, a stereospecific d-amino-acid decarboxylase Acta Crystallogr D 58 549 552
9. Levdikov V, Blagova L, Bose N, Momany C Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation (to be published)
10. Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK (2002) Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure 10:1499-1508
11. T Hu D Wu J Chen J Ding H Jiang X Shen 2008 The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis J Biol Chem 283 21284 21293
12. Zhu J, Swindell JT II, Chen L, Ebihara A, Shinkai A, Kuramitsu S, Yokoyama S, Fu Z-Q, Rose JP, Wang B-C Crystal structure of AQ1208 from Aquifex aeolicus (to be published)
13. Nakamura Y, Bessho Y, Padmanabhan B, Yokoyama S Crystal structure analysis of diaminopimelate decarboxylate (lysA) (to be published)
14. PJ White B Kelly 1965 Purification and properties of diaminopimelate decarboxylase from Escherichia coli Biochem J 96 75 84
15. G Kefala LJ Perry MS Weiss 2005 Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of LysA (Rv1293) from Mycobacterium tuberculosis Acta Crystallogr F 61 782 784 (Pubitemid 44210804)
16. Collaborative Computational Project, Number 4 1994 The CCP4 suite: programs for protein crystallography Acta Crystallogr D 50 760 763
17. A Vagin A Teplyakov 1997 MOLREP: An automated program for molecular replacement J Appl Crystallogr 30 1022 1025
18. GN Murshudov AA Vagin EJ Dodson 1997 Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr D 53 240 255
19. P Emsley K Cowtan 2004 Coot: model-building tools for molecular graphics Acta Crystallogr D 60 2126 2132
20. RJ Read 1986 Improved Fourier coefficients for maps using phases from partial structures with errors Acta Crystallogr A 42 140 149
21. RA Laskowski MW MacArthur DS Moss JM Thornton 1993 PROCHECK: a program to check the stereochemical quality of protein structures J Appl Crystallogr 26 283 291
22. W Kabsch 1976 A solution for the best rotation to relate two sets of vectors Acta Crystallogr D 32 922 923
23. E Krissinel K Henrick 2004 Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr D 60 2256 2268
24. W Kabsch C Sander 1983 Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 2577 2637
25. E Krissinel K Henrick 2007 Inference of macromolecular assemblies from crystalline state J Mol Biol 372 774 797
26. MW Roessle R Klaering U Ristau B Robrahn D Jahn T Gehrmann PV Konarev A Round S Fiedler C Hermes DI Svergun 2007 Upgrade of the small angle X-ray scattering beamline X33 at the EMBL Hamburg J Appl Crystallogr 40 s190 s194
27. PV Konarev VV Volkov AV Sokolova MHJ Koch DI Svergun 2003 PRIMUS: a windows PC-based system for small-angle scattering data analysis J Appl Crystallogr 36 1277 1282
28. D Svergun C Barberato MHJ Koch 1995 CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J Appl Crystallogr 28 768 773
29. M Brandl MS Weiss A Jabs J Sühnel R Hilgenfeld 2001 C-H•••π-interactions in proteins J Mol Biol 307 357 377
30. MS Weiss M Brandl J Sühnel D Pal R Hilgenfeld 2001 More hydrogen bonds for the (structural) biologist Trends Biochem Sci 26 521 523
31. Bevington PB (1969) Data reduction and error analysis for the physical sciences. McGraw-Hill, New York
32. G Schneider H Käck Y Lindqvist 2000 The manifold of vitamin B6 dependent enzymes Structure 8 R1 R6
33. G Kefala GL Evans MDW Griffin SRA Devenish FG Pearce MA Perugini JA Gerrard MS Weiss RCJ Dobson 2008 Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis Biochem J 411 351 360
34. Kefala G, Weiss MS (2006) Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis. Acta Crystallogr F 62:1116-1119. (Erratum in: Acta Crystallogr F 64:62)
35. G Kefala R Janowski S Panjikar C Mueller-Dieckmann MS Weiss 2005 Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapB (Rv2773c) from Mycobacterium tuberculosis Acta Crystallogr F 61 718 721 (Pubitemid 44210838)
36. M Cirilli R Zheng G Scapin JS Blanchard 2003 The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity Biochemistry 42 10644 10650
37. Janowski R, Kefala G, Weiss MS The structure of dihydrodipicolinate reductase (DapB, Rv2773c) from Mycobacterium tuberculosis in three crystal forms (to be published)
38. S Weyand G Kefala MS Weiss 2006 Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapC (Rv0858c) from Mycobacterium tuberculosis Acta Crystallogr F 62 794 797 (Pubitemid 44230246)
39. S Weyand G Kefala MS Weiss 2007 The three-dimensional structure of N-succinyl-diaminopimelate aminotransferase from Mycobacterium tuberculosis J Mol Biol 367 828 838
40. R Vyas V Kumar S Panjikar S Karthikeyan KV Radha Kishan R Tewari MS Weiss 2008 Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis Acta Crystallogr F 64 167 170
41. L Schuldt S Weyand G Kefala MS Weiss 2008 Cloning, expression, purification and preliminary X-ray diffraction analysis of tetrahydrodipicolinate-N-succinyltransferase (Rv1201c) from Mycobacterium tuberculosis Acta Crystallogr F 64 863 866
42. L Schuldt S Weyand G Kefala MS Weiss 2009 The three-dimensional structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism J Mol Biol 389 863 879
43. PJ Kraulis 1991 MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Crystallogr 24 946 950
44. EA Merritt DJ Bacon 1997 Raster3D: photorealistic molecular graphics Methods Enzymol 277 505 524
45. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos. http://www.pymol.org
46. J Lee AJ Michael D Martynowski EJ Goldsmith MA Phillips 2007 Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases J Biol Chem 282 27115 27125
47. R Shah R Akella EJ Goldsmith MA Phillips 2007 X-ray structure of paramecium bursaria chlorella virus arginine decarboxylase: insight into the structural basis for substrate specificity Biochemistry 46 2831 2841
48. Popovic B, Li Y, Chirgadze DY, Blundell TL, Spencer JB Structural characterisation of Btrk decarboxylase from Bacillus circulans butirosin biosynthesis (to be published)
49. NV Grishin AL Osterman HB Brooks MA Phillips EJ Goldsmith 1999 X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine Biochemistry 38 15174 15184
50. AD Kern MA Oliveira P Coffino ML Hackert 1999 Structure of mammalian ornithine decarboxylase at 1.6 Å resolution: stereochemical implications of PLP-dependent amino acid decarboxylases Structure 7 567 581
51. JJ Almrud MA Oliveira AD Kern NV Grishin MA Phillips ML Hackert 2000 Crystal structure of human ornithine decarboxylase at 2.1 Å resolution: structural insights to antizyme binding J Mol Biol 295 7 16