TRM13_YEAST
ID TRM13_YEAST Reviewed; 476 AA.
AC Q12383; D6W1U3;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=tRNA:m(4)X modification enzyme TRM13;
DE EC=2.1.1.225;
DE AltName: Full=tRNA methylase 13;
GN Name=TRM13; OrderedLocusNames=YOL125W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=8896265;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b%3c1013::aid-yea980%3e3.0.co;2-5;
RA Casamayor A., Khalid H., Balcells L., Aldea M., Casas C., Herrero E.,
RA Arino J.;
RT "Sequence analysis of a 13.4 kbp fragment from the left arm of chromosome
RT XV reveals a malate dehydrogenase gene, a putative Ser/Thr protein kinase,
RT the ribosomal L25 gene and four new open reading frames.";
RL Yeast 12:1013-1020(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [5]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=17242307; DOI=10.1261/rna.399607;
RA Wilkinson M.L., Crary S.M., Jackman J.E., Grayhack E.J., Phizicky E.M.;
RT "The 2'-O-methyltransferase responsible for modification of yeast tRNA at
RT position 4.";
RL RNA 13:404-413(2007).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro)
CC and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).
CC {ECO:0000269|PubMed:17242307}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Pro) + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(4) in tRNA(Pro) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:32767, Rhea:RHEA-COMP:10397, Rhea:RHEA-COMP:10398,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000269|PubMed:17242307};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-methionine = 2'-
CC O-methylcytidine(4) in tRNA(Gly)(GCC) + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:43192, Rhea:RHEA-COMP:10399, Rhea:RHEA-
CC COMP:10400, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000269|PubMed:17242307};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(4) in tRNA(His) + S-adenosyl-L-methionine = 2'-O-
CC methyladenosine(4) in tRNA(His) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43196, Rhea:RHEA-COMP:10401, Rhea:RHEA-COMP:10402,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74477; EC=2.1.1.225;
CC Evidence={ECO:0000269|PubMed:17242307};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 1230 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the methyltransferase TRM13 family.
CC {ECO:0000305}.
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DR EMBL; U41293; AAC49467.1; -; Genomic_DNA.
DR EMBL; Z74867; CAA99144.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10659.1; -; Genomic_DNA.
DR PIR; S63445; S63445.
DR RefSeq; NP_014516.1; NM_001183379.2.
DR AlphaFoldDB; Q12383; -.
DR BioGRID; 34250; 30.
DR IntAct; Q12383; 2.
DR MINT; Q12383; -.
DR STRING; 4932.YOL125W; -.
DR iPTMnet; Q12383; -.
DR MaxQB; Q12383; -.
DR PaxDb; Q12383; -.
DR PRIDE; Q12383; -.
DR EnsemblFungi; YOL125W_mRNA; YOL125W; YOL125W.
DR GeneID; 853995; -.
DR KEGG; sce:YOL125W; -.
DR SGD; S000005485; TRM13.
DR VEuPathDB; FungiDB:YOL125W; -.
DR eggNOG; KOG2811; Eukaryota.
DR GeneTree; ENSGT00390000003182; -.
DR HOGENOM; CLU_027610_1_0_1; -.
DR InParanoid; Q12383; -.
DR OMA; HRCSWRS; -.
DR BioCyc; MetaCyc:G3O-33521-MON; -.
DR BioCyc; YEAST:G3O-33521-MON; -.
DR BRENDA; 2.1.1.225; 984.
DR PRO; PR:Q12383; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q12383; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0052666; F:tRNA (cytosine-2'-O-)-methyltransferase activity; EXP:Reactome.
DR GO; GO:0106050; F:tRNA 2'-O-methyltransferase activity; IDA:SGD.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:SGD.
DR GO; GO:0002128; P:tRNA nucleoside ribose methylation; IMP:SGD.
DR InterPro; IPR007871; Methyltransferase_TRM13.
DR InterPro; IPR039044; Trm13.
DR InterPro; IPR022776; TRM13/UPF0224_CHHC_Znf_dom.
DR InterPro; IPR021721; Znf_CCCH-type_TRM13.
DR PANTHER; PTHR12998; PTHR12998; 1.
DR Pfam; PF05206; TRM13; 1.
DR Pfam; PF11722; zf-TRM13_CCCH; 1.
DR Pfam; PF05253; zf-U11-48K; 1.
DR PROSITE; PS51800; ZF_CHHC_U11_48K; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Metal-binding; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing; Zinc; Zinc-finger.
FT CHAIN 1..476
FT /note="tRNA:m(4)X modification enzyme TRM13"
FT /id="PRO_0000235932"
FT ZN_FING 72..99
FT /note="CHHC U11-48K-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT REGION 55..78
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 62..76
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 81
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
SQ SEQUENCE 476 AA; 54095 MW; 3280A732FFA374C1 CRC64;
MLQDNNGPAV KRAKPSERLQ CEYFMEKKKR RCGMTRSSQN LYCSEHLNLM KKAANSQVHN
KNGSEAEKER ERVPCPLDPN HTVWADQLKK HLKKCNKTKL SHLNDDKPYY EPGYNGENGL
LSSSVKIDIT AEHLVQSIEL LYKVFEGESM DELPLRQLNN KLMSLKRFPQ LPSNTKHAVQ
QSSLIENLVD AGAFERPESL NFIEFGCGRA EFSRYVSLYL LTQLTSLPAE HSGSNSNEFV
LIDRATNRMK FDKKIKDDFS EIKSNSPSKP ISCPSIKRIK IDIRDLKMDP ILKSTPGDDI
QYVCISKHLC GVATDLTLRC IGNSSILHGD DNNGCNPKLK AICIAMCCRH VCDYGDYVNR
SYVTSLVEKY RAHGSILTYE TFFRVLTKLC SWGTCGRKPG TAITDIVNVV ESFEGAEPYT
ITIKERENIG LMARRVIDEG RLVYVKEKFT EFNAELIRYV ESDVSLENVA MLVYKK
