A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 14, 2015, Pages 4310-4315

  Bunker, Richard D ^a,d   Mandal, Kalyaneswar ^b,c   Bashiri, Ghader ^a   Chaston, Jessica J ^a,b,d   Pentelute, Bradley L ^b,c,e   Lott, J Shaun ^a   Kent, Stephen B H ^b,f   Baker, Edward N ^a   Petsko, Gregory A ^g  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

^e VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^f MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^g WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Dormancy; Mycobacterium tuberculosis; Protein structure; Racemic protein crystallography; Ribosome binding

Indexed keywords

BACTERIAL PROTEIN; D DIMER; RV1738 PROTEIN; UNCLASSIFIED DRUG; PEPTIDE; RECOMBINANT PROTEIN;

ARTICLE; CIRCULAR DICHROISM; CRYSTALLIZATION; CRYSTALLOGRAPHY; ENANTIOMER; HIBERNATION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; RIBOSOME; SYNTHESIS; AMINO ACID SEQUENCE; CHEMISTRY; CONFORMATION; ESCHERICHIA COLI; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; STEREOISOMERISM; THERMUS; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; HUMANS; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PEPTIDES; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; RIBOSOMES; STEREOISOMERISM; THERMUS;

EID: 84929485510     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1422387112     Document Type: Article

References (38)

1. Corbett EL, et al. (2003) The growing burden of tuberculosis: Global trends and interactions with the HIV epidemic. Arch Intern Med 163(9): 1009-1021.
2. Parrish NM, Dick JD, Bishai WR (1998) Mechanisms of latency in Mycobacterium tuberculosis. Trends Microbiol 6(3): 107-112.
3. Wayne LG, Sohaskey CD (2001) Nonreplicating persistence of Mycobacterium tuberculosis. Annu Rev Microbiol 55: 139-163.
4. Hu YM, Butcher PD, Sole K, Mitchison DA, Coates ARM (1998) Protein synthesis is shutdown in dormant Mycobacterium tuberculosis and is reversed by oxygen or heat shock. FEMS Microbiol Lett 158(1): 139-145.
5. Pandey AK, Sassetti CM (2008) Mycobacterial persistence requires the utilization of host cholesterol. Proc Natl Acad Sci USA 105(11): 4376-4380.
6. Sherman DR, et al. (2001) Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding alpha-crystallin. Proc Natl Acad Sci USA 98(13): 7534-7539.
7. Voskuil MI, et al. (2003) Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J Exp Med 198(5): 705-713.
8. Sassetti CM, Boyd DH, Rubin EJ (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48(1): 77-84.
9. Yeates TO, Kent SBH (2012) Racemic protein crystallography. Annu Rev Biophys 41: 41-61.
10. Wukovitz SW, Yeates TO (1995) Why protein crystals favour some space-groups over others. Nat Struct Biol 2(12): 1062-1067.
11. Dawson PE, Muir TW, Clark-Lewis I, Kent SBH (1994) Synthesis of proteins by native chemical ligation. Science 266(5186): 776-779.
12. Kent SBH (2009) Total chemical synthesis of proteins. Chem Soc Rev 38(2): 338-351.
13. Mackay AL (1989) Crystal enigma. Nature 342: 133.
14. Moreland N, et al. (2005) A flexible and economical medium-throughput strategy for protein production and crystallization. Acta Crystallogr D Biol Crystallogr 61(Pt 10): 1378-1385.
15. Rayment I (1997) Reductive alkylation of lysine residues to alter crystallization properties of proteins. Methods Enzymol 276: 171-179.
16. Cooper DR, et al. (2007) Protein crystallization by surface entropy reduction: Optimization of the SER strategy. Acta Crystallogr D Biol Crystallogr 63(Pt 5): 636-645.
17. Yan LZ, Dawson PE (2001) Synthesis of peptides and proteins without cysteine residues by native chemical ligation combined with desulfurization. J Am Chem Soc 123(4): 526-533.
18. Pentelute BL, Kent SB (2007) Selective desulfurization of cysteine in the presence of Cys(Acm) in polypeptides obtained by native chemical ligation. Org Lett 9(4): 687-690.
19. Rodríguez DD, et al. (2009) Crystallographic ab initio protein structure solution below atomic resolution. Nat Methods 6(9): 651-653.
20. McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Cryst 40(Pt 4): 658-674.
21. Luzzati V (1952) Traitement statistique des erreurs dans la determination des structuresbcristallines. Acta Crystallogr 5: 802-810.
22. Murshudov GN, et al. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67(Pt 4): 355-367.
23. Cowtan K (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 62(Pt 9): 1002-1011.
24. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66(Pt 4): 486-501.
25. Adams PD, et al. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2): 213-221.
26. Chen VB, et al. (2010) MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1): 12-21.
27. Finn RD, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38(Database issue, Suppl. 1):D211-D222.
28. Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1): 2256-2268.
29. Ye K, Serganov A, Hu W, Garber M, Patel DJ (2002) Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur J Biochem 269(21): 5182-5191.
30. Rak A, Kalinin A, Shcherbakov D, Bayer P (2002) Solution structure of the ribosomeassociated cold shock response protein Yfia of Escherichia coli. Biochem Biophys Res Commun 299(5): 710-714.
31. Sato A, et al. (2009) Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function. Biochem Biophys Res Commun 389(4): 580-585.
32. De Bari H, Berry EA (2013) Structure of Vibrio cholerae ribosome hibernation promoting factor. Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 3): 228-236.
33. Vila-Sanjurjo A, Schuwirth B-S, Hau CW, Cate JHD (2004) Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol 11(11): 1054-1059.
34. Polikanov YS, Blaha GM, Steitz TA (2012) How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science 336(6083): 915-918.
35. Matthews BW (2009) Racemic crystallography - easy crystals and easy structures: What's not to like? Protein Sci 18(6): 1135-1138.
36. Zawadzke LE, Berg JM (1993) The structure of a centrosymmetric protein crystal. Proteins 16(3): 301-305.
37. Park HD, et al. (2003) Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol Microbiol 48(3): 833-843.
38. Trauner A, Lougheed KEA, Bennett MH, Hingley-Wilson SM, Williams HD (2012) The dormancy regulator DosR controls ribosome stability in hypoxic mycobacteria. J Biol Chem 287(28): 24053-24063.