Abstract
Advancement in technology has helped to solve structures of several proteins including M. tuberculosis (MTB) proteins. Identifying similarity between protein structures could not only yield valuable clues to their function, but can also be employed for motif finding, protein docking and off-target identification. The current study has undertaken analysis of structures of all MTB gene products with available structures was analyzed. Majority of the MTB proteins belonged to the α/β class. 23 different protein folds are used in the MTB protein structures. Of these, the TIM barrel fold was found to be highly conserved even at very low sequence identity. We identified 21 paralogs and 27 analogs of MTB based on domains and EC classification. Our analysis revealed that many of the current drug targets share structural similarity with other proteins within the MTB genome, which could probably be off-targets. Results of this analysis have been made available in the Mycobacterium tuberculosis Structural Database (http://bmi.icmr.org.in/mtbsd/MtbSD.php/search.php) which is a useful resource for current and novel drug targets of MTB.
Similar content being viewed by others
References
Mativandlela SP, Lall N, Meyer JJ (2008) Antibacterial, antifungal and antitubercular activity of (the roots of) Pelargonium reniforme (CURT) and Pelargonium sidoides (DC) (Geraniaceae) root extracts. S Afr J Bot 72:232–237
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393(6685):537–544
Eisenberg D, Marcotte EM, Xenarios I, Yeates TO (2000) Protein function in the post-genomic era. Nature 405(6788):823–826
Kim SH (2000) Structural genomics of microbes: an objective. Curr Opin Struct Biol 10(3):380–383
Ioerger TR, Sacchettini JC (2009) Structural genomics approach to drug discovery for Mycobacterium tuberculosis. Curr Opin Microbiol 12(3):318–325
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823–826
Koonin EV, Wolf YI, Karev GP (2002) The structure of the protein universe and genome evolution. Nature 420(6912):218–223
Chen L, Wu LY, Wang Y, Zhang S, Zhang XS (2006) Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Struct Biol 6:18
Sierk ML, Kleywegt GJ (2004) Deja vu all over again: finding and analyzing protein structure similarities. Structure 12(12):2103–2111
Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res 39 (Database issue):D392-401
Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247(4):536–540
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
Farber GK, Petsko GA (1990) The evolution of alpha/beta barrel enzymes. Trends Biochem Sci 15(6):228–234
Branden CI (1991) The TIM barrel—the most frequently occurring folding motif in proteins. Curr Opin Struct Biol 1:978–83
Wilmanns M, Hyde CC, Davies DR, Kirschner K, Jansonius JN (1991) Structural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry 30(38):9161–9169
Nagano N, Hutchinson EG, Thornton JM (1999) Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels. Protein Sci 8(10):2072–2084
Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M (2000) Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 289(5484):1546–1550
Chaudhuri BN, Sawaya MR, Kim CY, Waldo GS, Park MS, Terwilliger TC, Yeates TO (2003) The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis. Structure 11(7):753–764
Rho BS, Hung LW, Holton JM, Vigil D, Kim SI, Park MS, Terwilliger TC, Pedelacq JD (2006) Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis. J Mol Biol 361(5):850–863
Guimaraes BG, Souchon H, Honore N, Saint-Joanis B, Brosch R, Shepard W, Cole ST, Alzari PM (2005) Structure and mechanism of the alkyl hydroperoxidase AhpC, a key element of the Mycobacterium tuberculosis defense system against oxidative stress. J Biol Chem 280(27):25735–25742
Li S, Peterson NA, Kim MY, Kim CY, Hung LW, Yu M, Lekin T, Segelke BW, Lott JS, Baker EN (2005) Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin. J Mol Biol 346(4):1035–1046
Goulding CW, Apostol MI, Gleiter S, Parseghian A, Bardwell J, Gennaro M, Eisenberg D (2004) Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. a structure to function analysis of DsbE from Mycobacterium tuberculosis. J Biol Chem 279(5):3516–3524
Cheng X, Roberts RJ (2001) AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res 29(18):3784–3795
Boissier F, Bardou F, Guillet V, Uttenweiler-Joseph S, Daffe M, Quemard A, Mourey L (2006) Further insight into S-adenosylmethionine-dependent methyltransferases: structural characterization of Hma, an enzyme essential for the biosynthesis of oxygenated mycolic acids in Mycobacterium tuberculosis. J Biol Chem 281(7):4434–4445
Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J et al (1992) The alpha/beta hydrolase fold. Protein Eng 5(3):197–211
Wilson RA, Maughan WN, Kremer L, Besra GS, Futterer K (2004) The structure of Mycobacterium tuberculosis MPT51 (FbpC1) defines a new family of non-catalytic alpha/beta hydrolases. J Mol Biol 335(2):519–530
Lesk AM (1995) NAD-binding domains of dehydrogenases. Curr Opin Struct Biol 5(6):775–783
Yang S, Doolittle RF, Bourne PE (2005) Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A 102(2):373–378
Quemard A, Sacchettini JC, Dessen A, Vilcheze C, Bittman R, Jacobs WR Jr, Blanchard JS (1995) Enzymatic characterization of the target for isoniazid in Mycobacterium tuberculosis. Biochemistry 34(26):8235–8241
Marrakchi H, Laneelle G, Quemard A (2000) InhA, a target of the antituberculous drug isoniazid, is involved in a mycobacterial fatty acid elongation system, FAS-II. Microbiology 146(Pt 2):289–296
Oliveira JS, Pereira JH, Canduri F, Rodrigues NC, de Souza ON, de Azevedo WF Jr, Basso LA, Santos DS (2006) Crystallographic and pre-steady-state kinetics studies on binding of NADH to wild-type and isoniazid-resistant enoyl-ACP(CoA) reductase enzymes from Mycobacterium tuberculosis. J Mol Biol 359(3):646–666
Kapur V, Li LL, Hamrick MR, Plikaytis BB, Shinnick TM, Telenti A, Jacobs WR Jr, Banerjee A, Cole S, Yuen KY et al (1995) Rapid Mycobacterium species assignment and unambiguous identification of mutations associated with antimicrobial resistance in Mycobacterium tuberculosis by automated DNA sequencing. Arch Pathol Lab Med 119(2):131–138
Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ (2008) MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res 36 (Web Server issue):W260-264
Russell RB, Saqi MA, Sayle RA, Bates PA, Sternberg MJ (1997) Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol 269(3):423–439
Sonnhammer EL, Koonin EV (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet 18(12):619–620
Hassan S, Logambiga P, Raman AM, Subazini TK, Kumaraswami V, Hanna LE MtbSD-A comprehensive structural database for Mycobacterium tuberculosis. Tuberculosis (Edinb).
Orengo CA, Todd AE, Thornton JM (1999) From protein structure to function. Curr Opin Struct Biol 9(3):374–382
Orengo CA, Jones DT, Thornton JM (1994) Protein superfamilies and domain superfolds. Nature 372(6507):631–634
Acknowledgments
The authors wish to acknowledge Indian Council of Medical Research (ICMR) - Biomedical Informatics and National Institute for Research in Tuberculosis for the funding provided. We also thank Mr. Senthilnathan, National Institute for Research in Tuberculosis (NIRT) for editing figures.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Hassan, S., Debnath, A., Mahalingam, V. et al. Computational structural analysis of proteins of Mycobacterium tuberculosis and a resource for identifying off-targets. J Mol Model 18, 3993–4004 (2012). https://doi.org/10.1007/s00894-012-1412-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00894-012-1412-5