title: Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site.
abstract: 2'-O-ribose methylation is one of the most common posttranscriptional modifications in RNA. Methylations at different positions are introduced by enzymes from at least two unrelated superfamilies. Recently, a new family of eukaryotic RNA methyltransferases (MTases) has been identified, and its representative from yeast (Yol125w, renamed as Trm13p) has been shown to 2'-O-methylate position 4 of tRNA. Trm13 is conserved in Eukaryota, but exhibits no sequence similarity to other known MTases. Here, I present the results of bioinformatics analysis which suggest that Trm13 is a strongly diverged member of the Rossmann-fold MTase (RFM) superfamily, and therefore is evolutionarily related to 2'-O-MTases such as Trm7 and fibrillarin. However, the character of conserved residues in the predicted active site of the Trm13 family suggests it may use a different mechanism of ribose methylation than its relatives. A molecular model of the Trm13p structure has been constructed and evaluated for potential accuracy using model quality assessment methods. The predicted structure will facilitate experimental analyses of the Trm13p mechanism of action.
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4,Warsaw, Poland. karolina_tkaczuk@go2.pl
authors.forename: Karolina L
authors.initials: KL
authors.lastname: Tkaczuk
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D003545:Cysteine; D006639:Histidine; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D012343:RNA, Transfer / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012359:tRNA Methyltransferases / Q000737:chemistry*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D006639:Histidine; D012343:RNA, Transfer; C518889:TRM13 protein, S cerevisiae; D012359:tRNA Methyltransferases; D003545:Cysteine
references.citation: J Mol Biol. 1999 Apr 9;287(4):797-815
references.pmid: 10191147
references.citation: Proteins. 2004 Jun 1;55(4):1005-13
references.pmid: 15146497
references.citation: Trends Biochem Sci. 2003 Jun;28(6):329-35
references.pmid: 12826405
references.citation: Nucleic Acids Res. 2006 Apr 05;34(6):1925-34
references.pmid: 16600901
references.citation: BMC Bioinformatics. 2002 Apr 03;3:10
references.pmid: 11929612
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3305-7
references.pmid: 12824313
references.citation: J Mol Biol. 1997 Apr 25;268(1):209-25
references.pmid: 9149153
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D145-9
references.pmid: 16381833
references.citation: Biochemistry. 1991 Oct 8;30(40):9724-8
references.pmid: 1911760
references.citation: Biochemistry. 1998 May 19;37(20):7103-12
references.pmid: 9585521
references.citation: Nucleic Acids Res. 2004 Apr 30;32(8):2453-63
references.pmid: 15121902
references.citation: J Mol Biol. 2000 Jun 2;299(2):499-520
references.pmid: 10860755
references.citation: Bioinformatics. 2008 Oct 15;24(20):2277-80
references.pmid: 18703587
references.citation: Biotechniques. 1993 Jun;14(6):1010-3
references.pmid: 8333944
references.citation: J Mol Biol. 2001 Jun 29;310(1):243-57
references.pmid: 11419950
references.citation: BMC Mol Biol. 2006 Jul 18;7:23
references.pmid: 16848900
references.citation: Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8263-5
references.pmid: 10899996
references.citation: Cell. 1993 Feb 12;72(3):443-57
references.pmid: 8431947
references.citation: Biochimie. 2005 Sep-Oct;87(9-10):889-95
references.pmid: 16164996
references.citation: Proteins. 2005;61 Suppl 7:106-13
references.pmid: 16187351
references.citation: BMC Evol Biol. 2006 Jan 24;6:6
references.pmid: 16433904
references.citation: Proteins. 2003;53 Suppl 6:352-68
references.pmid: 14579324
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
references.pmid: 15980461
references.citation: Proteins. 2005 May 15;59(3):482-8
references.pmid: 15789416
references.citation: Gene. 2003 Jan 2;302(1-2):129-38
references.pmid: 12527203
references.citation: BMC Struct Biol. 2005 Oct 14;5:19
references.pmid: 16225687
references.citation: J Mol Biol. 1999 Jun 4;289(2):277-91
references.pmid: 10366505
references.citation: Proteins. 2001 Dec 1;45(4):397-407
references.pmid: 11746687
references.citation: Nucleic Acids Res. 2007;35(13):4264-74
references.pmid: 17576679
references.citation: Mol Cell. 2004 Jan 16;13(1):77-89
references.pmid: 14731396
references.citation: Nat Struct Biol. 1997 Jun;4(6):483-9
references.pmid: 9187657
references.citation: J Mol Biol. 2001 Mar 16;307(1):447-63
references.pmid: 11243830
references.citation: Mol Cell. 2004 Nov 19;16(4):663-9
references.pmid: 15546625
references.citation: EMBO J. 2002 Apr 2;21(7):1811-20
references.pmid: 11927565
references.citation: J Biol Chem. 1987 Apr 5;262(10):4778-86
references.pmid: 3558369
references.citation: Protein Sci. 2001 Nov;10(11):2354-62
references.pmid: 11604541
references.citation: EMBO J. 2002 Mar 1;21(5):1139-47
references.pmid: 11867542
references.citation: BMC Bioinformatics. 2007 Mar 05;8:73
references.pmid: 17338813
references.citation: Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41
references.pmid: 11517324
references.citation: J Bacteriol. 2004 Oct;186(19):6634-42
references.pmid: 15375145
references.citation: J Mol Biol. 2004 May 28;339(2):337-53
references.pmid: 15136037
references.citation: Protein Sci. 2006 Apr;15(4):900-13
references.pmid: 16522791
references.citation: Proteins. 2005;61 Suppl 7:128-34
references.pmid: 16187354
references.citation: Proteins. 2005;61 Suppl 7:46-66
references.pmid: 16187346
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Proteins. 2003;53 Suppl 6:534-41
references.pmid: 14579343
references.citation: Bioinformatics. 2003 Jan;19(1):163-4
references.pmid: 12499312
references.citation: RNA. 1999 Jan;5(1):66-81
references.pmid: 9917067
references.citation: Proteins. 2003 May 15;51(3):434-41
references.pmid: 12696054
references.citation: RNA. 2007 Mar;13(3):404-13
references.pmid: 17242307
references.citation: Protein Sci. 2000 Feb;9(2):232-41
references.pmid: 10716175
references.citation: BMC Bioinformatics. 2008 Sep 29;9:403
references.pmid: 18823532