RNA: (guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - Bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure

BMC Bioinformatics

Volumn 3, Issue , 2002, Pages

  Bujnicki, Janusz M ^a   Rychlewski, Leszek ^b  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^b BIOINFOBANK INSTITUTE   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; GUANINE NUCLEOTIDE; PROTEIN MJ0882; RIBOSOME RNA; RNA METHYLTRANSFERASE; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN; ESCHERICHIA COLI PROTEIN; GUANINE; METHYLTRANSFERASE; RSMC PROTEIN, E COLI; TRANSFER RNA METHYLTRANSFERASE;

ALGORITHM; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOINFORMATICS; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; CONTROLLED STUDY; ENZYME ACTIVE SITE; GENE IDENTIFICATION; GENETIC CONSERVATION; METHANOCOCCUS JANNASCHII; NONHUMAN; PREDICTION; PROTEIN BINDING; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENZYMOLOGY; GENETICS; METABOLISM; METHANOCOCCUS; METHODOLOGY; MOLECULAR EVOLUTION; PHYSIOLOGY; PREDICTION AND FORECASTING; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

ARCHAEA; ESCHERICHIA COLI; EUKARYOTA; POSIBACTERIA;

ARCHAEAL PROTEINS; BINDING SITES; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GUANINE; METHANOCOCCUS; METHYLTRANSFERASES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PREDICTIVE VALUE OF TESTS; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRNA METHYLTRANSFERASES;

EID: 0012588361     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-3-10     Document Type: Article

References (57)

1. Rozenski J, Crain PF, McCloskey JA: The RNA Modification Database: 1999 update. Nucleic Acids Res. 1999, 27:196-197
2. Anderson J, Phan L, Hinnebusch AG: The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci U.S.A. 2000, 97:5173-5178
3. 2+ in RNA structure and function. Prog. Nucleic Acid Res. Mol. Biol 1996, 53:79-129
4. Raue HA, Klootwijk J, Musters W: Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. Prog. Biophys. Mol. Biol 1988, 51:77-129
5. von Ahsen U, Noller HF: Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science 1995, 267:234-237
6. Murgola EJ, Hijazi KA, Goringer HU, Dahlberg AE: Mutant 16S ribosomal RNA: a codon-specific translational suppressor. Proc. Natl. Acad. Sci U.S.A. 1988, 85:4162-4165
7. Carter AP, demons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishan V: Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 2000, 407:340-348
8. Cunningham PR, Richard RB, Weitzmann CJ, Nurse K, Ofengand J: The absence of modified nucleotides affects both in vitro assembly and in vitro function of the 30S ribosomal subunit of Escherichia coli. Biochimie 1991, 73:789-796
9. Weitzmann C, Tumminia SJ, Boublik M, Ofengand J: A paradigm for local conformational control of function in the ribosome: binding of ribosomal protein S19 to Escherichia coli 16S rRNA in the presence of S7 is required for methylation of m2G966 and blocks methylation of m5C967 by their respective methyltransferases. Nucleic Acids Res. 1991, 19:7089-7095
10. 2G1207 methyltransferase from Escherichia coli. J Biol Chem. 1999, 274:924-929
11. Bujnicki JM: Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. FASEB J 2000, 14:2365-2368
12. Fauman EB, Blumenthal RM, Cheng X: Structure and evolution of AdoMet-dependent MTases. In S-Adenosylmethionine-dependent methyltransferases: structures and functions. 1999, 1-38
13. 1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. J. Mol. Microbiol. Biotechnol. 2002, 4:93-99
14. Nakahigashi K, Kubo N, Narita SS, Shimaoka T, Goto S, Oshima T, Mori H, Maeda M, Wada C, Inokuchi H: HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc. Natl. Acad. Sci. U.S.A 2002, 99:1473-1478
15. Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH: The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 2002, 21:769-778
16. Aravind L, Koonin EV: Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol. 1999, 287:1023-1040
17. Rychlewski L, Jaroszewski L, Li W, Godzik A: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9:232-241
18. Neuwald AF, Liu JS, Lipman DJ, Lawrence CE: Extracting protein alignment models from the sequence database. Nucleic Acids Res. 1997, 25:1665-1677
19. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425
20. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28:235-242
21. Gibrat JF, Madej T, Bryant SH: Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 1996, 6:377-385
22. Holm L, Sander C: Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 1993, 233:123-138
23. Bujnicki JM: Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol. 1999, 1:1-8 [http://www.bioinfo.de/isb/1999-01/0016/]
24. Schluckebier G, Zhong P, Stewart KD, Kavanaugh TJ, Abad-Zapatero C: The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J. Mol. Biol. 1999, 289:277-291
25. Schluckebier G, Kozak M, Bleimling N, Weinhold E, Saenger W: Differential binding of S-adenosylmethionine S-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M. TaqI. J Mol. Biol. 1997, 265:56-67
26. Vidgren J, Svensson LA, Liljas A: Crystal structure of catechol Omethyltransferase. Nature 1994, 368:354-358
27. Goodsell DS, Morris GM, Olson AJ: Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recognit. 1996, 9:1-5
28. Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, Saper MA, Bardwell JC, Jakob U: RNA methylation under heat shock control. Mol. Cell 2000, 6:349-360
29. Goedecke K, Pignot M, Goody RS, Scheidig AJ, Weinhold E: Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat. Struct. Biol 2001, 8:121-125
30. Schluckebier G, Labahn J, Granzin J, Saenger W: M.TaqI: possible catalysis via cation-pi interactions in N-specific DNA methyltransferases. Biol. Chem. 1998, 379:389-400
31. Klimasauskas S, Kumar S, Roberts RJ, Cheng X: HhaI methyltransferase flips its target base out of the DNA helix. Cell 1994, 76:357-369
32. Cheng X, Roberts RJ: AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 2001, 29:3784-3795
33. Gammie AE, Stewart BG, Scott CF, Rose MD: The two forms of karyogamy transcription factor Kar4p are regulated by differential initiation of transcription, translation, and protein turnover. Mol. Cell Biol 1999, 19:817-825
34. Bujnicki JM: In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett. 2001, 507:123-127
35. Gupta A, Kumar PH, Dineshkumar TK, Varshney U, Subramanya HS: Crystal structure of Rv2118c: An AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv. J Mol. Biol 2001, 312:381-391
36. Todd AE, Orengo CA, Thornton JM: Evolution of function in protein superfamilies, from a structural perspective. J Mol. Biol 2001, 307:1113-1143
37. 5C DNA methyltransferases use different cysteine residues as catalysts. Proc. Natl. Acad. Sci U.S.A. 2000, 97:8263-8265
38. Bujnicki JM, Feder M, Radlinska M, Rychlewski L: mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics 2001, 2:2
39. Li H, Trotta CR, Abelson J: Crystal structure and evolution of a transfer RNA splicing enzyme. Science 1998, 280:279-284
40. Li H, Abelson J: Crystal structure of a dimeric archaeal splicing endonuclease. J Mol. Biol 2000, 302:639-648
41. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402
42. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001, 29:2994-3005
43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882
44. Bujnicki JM, Elofsson A, Fischer D, L Rychlewski: Structure prediction Meta Server. Bioinformatics 2001, 17:750-751
45. Kelley LA, McCallum CM, Sternberg MJ: Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol. 2000, 299:499-520
46. Fischer D: Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac. Symp. Biocomput. 2000, 119-130
47. Jones DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol. Biol 1999, 287:797-815
48. Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R: Predicting protein structure using only sequence information. Proteins. 1999, Suppl 3:121-125
49. Shi J, Blundell TL, Mizuguchi K: Fugue: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol. Biol. 2001, 310:243-257
50. Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ: JPred: a consensus secondary structure prediction server. Bioinformatics 1998, 14:892-893
51. McGuffin LJ, Bryson K, Jones DT: The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-405
52. Lundstrom J, Rychlewski L, Bujnicki JM, Elofsson A: Pcons: A neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001, 10:2354-2362
53. Holm L, Sander C: Dali: a network tool for protein structure comparison. Trends. Biochem. Sci. 1995, 20:478-480
54. Guex N, Peitsch MC: SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 1997, 18:2714-2723
55. Scavetta RD, Thomas CB, Walsh MA, Szegedi S, Joachimiak A, Gumport RI, Churchill ME: Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases. Nucleic Acids Res. 2000, 28:3950-3961
56. Tran PH, Korszun ZR, Cerritelli S, Springhorn SS, Lacks SA: Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine. Structure 1998, 6:1563-1575
57. Gong W, O'Gara M, Blumenthal RM, Cheng X: Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 1997, 25:2702-2715