Structural Insights into Putative Molybdenum Cofactor Biosynthesis Protein C (MoaC2) from Mycobacterium tuberculosis H37Rv

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Srivastava, Vijay Kumar ^a   Srivastava, Shubra ^a   Arora, Ashish ^a   Pratap, J Venkatesh ^a  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MICROORGANISM PROTEIN; MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN A1; MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN C2; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; MOLECULAR DOCKING; MYCOBACTERIUM TUBERCULOSIS; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; COENZYMES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENZYMES; METALLOPROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PTERIDINES; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84875120605     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058333     Document Type: Article

References (47)

1. Wuebbens MM, Rajagopalan KV, (1995) Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. The Journal of biological chemistry 270: 1082-1087.
2. Rieder C, Eisenreich W, O'Brien J, Richter G, Gotze E, et al. (1998) Rearrangement reactions in the biosynthesis of molybdopterin-an NMR study with multiply 13C/15N labelled precursors. European journal of biochemistry 255: 24-36.
3. Srivastava S, Srivastava VK, Arora A, Pratap JV, (2012) Overexpression, purification,crystallization and preliminary X-ray analysis of putative molybdenum cofactor biosynthesis protein C (MoaC2) from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 687-691.
4. Frey PA, Magnusson OT, (2003) S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin? Chemical reviews 103: 2129-2148.
5. Jarrett JT, (2003) The generation of 5′-deoxyadenosyl radicals by adenosylmethionine-dependent radical enzymes. Current opinion in chemical biology 7: 174-182.
6. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE, (2001) Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic acids research 29: 1097-1106.
7. Hanzelmann P, Schindelin H, (2006) Binding of 5′-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism. Proceedings of the National Academy of Sciences of the United States of America 103: 6829-6834.
8. Kanaujia SP, Jeyakanthan J, Nakagawa N, Balasubramaniam S, Shinkai A, et al. (2010) Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8. Acta crystallographica 66: 821-833.
9. Reiss J, Cohen N, Dorche C, Mandel H, Mendel RR, et al. (1998) Mutations in a polycistronic nuclear gene associated with molybdenum cofactor deficiency. Nature genetics 20: 51-53.
10. Hoff T, Schnorr KM, Meyer C, Caboche M, (1995) Isolation of two Arabidopsis cDNAs involved in early steps of molybdenum cofactor biosynthesis by functional complementation of Escherichia coli mutants. The Journal of biological chemistry 270: 6100-6107.
11. Unkles SE, Smith J, Kanan GJ, Millar LJ, Heck IS, et al. (1997) The Aspergillus nidulans cnxABC locus is a single gene encoding two catalytic domains required for synthesis of precursor Z, an intermediate in molybdenum cofactor biosynthesis. The Journal of biological chemistry 272: 28381-28390.
12. Hanzelmann P, Schwarz G, Mendel RR, (2002) Functionality of alternative splice forms of the first enzymes involved in human molybdenum cofactor biosynthesis. The Journal of biological chemistry 277: 18303-18312.
13. Rudolph MJ, Wuebbens MM, Rajagopalan KV, Schindelin H, (2001) Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation. Nature structural biology 8: 42-46.
14. Leimkuhler S, Wuebbens MM, Rajagopalan KV, (2001) Characterization of Escherichia coli MoeB and its involvement in the activation of molybdopterin synthase for the biosynthesis of the molybdenum cofactor. The Journal of biological chemistry 276: 34695-34701.
15. Wuebbens MM, Liu MT, Rajagopalan K, Schindelin H, (2000) Insights into molybdenum cofactor deficiency provided by the crystal structure of the molybdenum cofactor biosynthesis protein MoaC. Structure 8: 709-718.
16. Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K, (2002) Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Molecular microbiology 43: 717-731.
17. Wuebbens MM, Rajagopalan KV, (1993) Structural characterization of a molybdopterin precursor. The Journal of biological chemistry 268: 13493-13498.
18. Dutta NK, Mehra S, Didier PJ, Roy CJ, Doyle LA, et al. (2010) Genetic Requirements for the Survival of Tubercle Bacilli in Primates. The Journal of infectious disease 201: 1743-1752.
19. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. Journal of molecular biology 372: 774-797.
20. Yoshida H, Yamada M, Kuramitsu S, Kamitori S, (2008) Structure of a putative molybdenum-cofactor biosynthesis protein C (MoaC) from Sulfolobus tokodaii (ST0472). Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 589-592.
21. Hanzelmann P, Schindelin H, (2004) Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proceedings of the National Academy of Sciences of the United States of America 101: 12870-12875.
22. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database: functional interaction networks of proteins, globally integrated and scored. Nucleic acids research 39: D561-568.
23. Arnold K, Bordoli L, Kopp J, Schwede T, (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics (Oxford, England) 22: 195-201.
24. Bradford JR, Westhead DR, (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (Oxford, England) 21: 1487-1494.
25. Tina KG, Bhadra R, Srinivasan N, (2007) PIC: Protein Interactions Calculator. Nucleic acids research 35: W473-476.
26. Battye TG, Kontogiannis L, Johnson O, Powell HR, Leslie AG, (2011) iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta crystallographica D 67: 271-281.
27. Evans P, (2006) Scaling and assessment of data quality. Acta crystallographica 62: 72-82.
28. French S, Wilson K, (1978) On the treatment of negative intensity observations. Acta Cryst A 34: 517-525.
29. Otwinowski Z, Minor W, (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology 276: 307-326.
30. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Cryst 40: 658-674.
31. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta Cryst 67: 235-242.
32. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, et al. (2010) Acta Crystallogr D 66: 213-221.
33. Brunger AT, (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472-475.
34. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta crystallographica 60: 2126-2132.
35. Ramachandran GN, Sasisekharan V, (1968) Conformation of polypeptides and proteins. Advances in protein chemistry 23: 283-438.
36. Laskowski RA, MacArthur MW, Moss DS, Thornton JM, (1993) A program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283-291.
37. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta crystallographica D 66: 12-21.
38. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic acids research 28: 235-242.
39. Goodsell DS, Morris GM, Olson AJ, (1996) Automated docking of flexible ligands:applications of AutoDock. J Mol Recognit 9: 1-5.
40. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J Computational Chemistry 19: 1639-1662.
41. ACCELRYS ver. 1.1. San Diego CA Accelrys (2000). 92121-92152.
42. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic acids research 31: 258-261.
43. von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, et al. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic acids research 33: D433-437.
44. Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, et al. (2007) ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins 69: 781-785.
45. Russell RB, Barton GJ, (1992) Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14: 309-323.
46. Thomson JD, Higgins DG, Gibson TJ, (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22 (22):: 4673-80.
47. Gouet P, Courcelle E, Stuart DI, Metoz F, (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15: 305-308.