NCL1_YEAST
ID NCL1_YEAST Reviewed; 684 AA.
AC P38205; D6VPX6;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Multisite-specific tRNA:(cytosine-C(5))-methyltransferase;
DE EC=2.1.1.202;
DE AltName: Full=Multisite-specific tRNA:m5C-methyltransferase;
DE AltName: Full=tRNA (cytosine-5-)-methyltransferase NCL1;
DE AltName: Full=tRNA methyltransferase 4;
GN Name=NCL1; Synonyms=TRM4; OrderedLocusNames=YBL024W; ORFNames=YBL0437;
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 204508 / S288c;
RX PubMed=7725803; DOI=10.1002/yea.320101217;
RA van Dyck L., Jonniaux J.-L., Barreiros T.D.M., Kleine K., Goffeau A.;
RT "Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the
RT ribosomal protein L19 as well as proteins with homologies to components of
RT the hnRNP and snRNP complexes and to the human proliferation-associated
RT p120 antigen.";
RL Yeast 10:1663-1673(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
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 FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=9767141; DOI=10.1016/s0378-1119(98)00330-8;
RA Wu P., Brockenbrough J.S., Paddy M.R., Aris J.P.;
RT "NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces
RT cerevisiae.";
RL Gene 220:109-117(1998).
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=10445884; DOI=10.1017/s1355838299982201;
RA Motorin Y., Grosjean H.;
RT "Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast
RT Saccharomyces cerevisiae: identification of the gene and substrate
RT specificity of the enzyme.";
RL RNA 5:1105-1118(1999).
RN [6]
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 [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-431, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-426 AND SER-667, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Methylates cytosine to m5C at several positions in different
CC tRNAs and pre-tRNAs containing intron. Able to modify tRNAs at all four
CC positions (34, 40, 48 and 49) at which m5C has been found in tRNAs. May
CC be involved in ribosome biogenesis as its disruption leads to increased
CC sensitivity to the antibiotic paromomycin.
CC {ECO:0000269|PubMed:10445884, ECO:0000269|PubMed:9767141}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(34) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(34) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:42940, Rhea:RHEA-COMP:10291, Rhea:RHEA-
CC COMP:10295, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.202;
CC Evidence={ECO:0000269|PubMed:10445884};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(40) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(40) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:42944, Rhea:RHEA-COMP:10292, Rhea:RHEA-
CC COMP:10296, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.202;
CC Evidence={ECO:0000269|PubMed:10445884};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(48) in tRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(48) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42948, Rhea:RHEA-COMP:10293, Rhea:RHEA-COMP:10297,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.202;
CC Evidence={ECO:0000269|PubMed:10445884};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(49) in tRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(49) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42952, Rhea:RHEA-COMP:10294, Rhea:RHEA-COMP:10385,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.202;
CC Evidence={ECO:0000269|PubMed:10445884};
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:9767141}.
CC -!- MISCELLANEOUS: Present with 16100 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. TRM4 subfamily. {ECO:0000255|PROSITE-
CC ProRule:PRU01023}.
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DR EMBL; X77291; CAA54502.1; -; Genomic_DNA.
DR EMBL; Z35785; CAA84843.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07096.1; -; Genomic_DNA.
DR PIR; S45758; S45758.
DR RefSeq; NP_009529.1; NM_001178264.1.
DR AlphaFoldDB; P38205; -.
DR SMR; P38205; -.
DR BioGRID; 32674; 213.
DR DIP; DIP-3932N; -.
DR IntAct; P38205; 23.
DR MINT; P38205; -.
DR STRING; 4932.YBL024W; -.
DR iPTMnet; P38205; -.
DR MaxQB; P38205; -.
DR PaxDb; P38205; -.
DR PRIDE; P38205; -.
DR EnsemblFungi; YBL024W_mRNA; YBL024W; YBL024W.
DR GeneID; 852257; -.
DR KEGG; sce:YBL024W; -.
DR SGD; S000000120; NCL1.
DR VEuPathDB; FungiDB:YBL024W; -.
DR eggNOG; KOG2198; Eukaryota.
DR GeneTree; ENSGT00940000153665; -.
DR HOGENOM; CLU_005316_4_3_1; -.
DR InParanoid; P38205; -.
DR OMA; QLFTEYV; -.
DR BioCyc; MetaCyc:G3O-28927-MON; -.
DR BioCyc; YEAST:G3O-28927-MON; -.
DR BRENDA; 2.1.1.202; 984.
DR PRO; PR:P38205; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38205; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0008168; F:methyltransferase activity; IBA:GO_Central.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IDA:SGD.
DR GO; GO:0000049; F:tRNA binding; IDA:SGD.
DR GO; GO:0070301; P:cellular response to hydrogen peroxide; IMP:SGD.
DR GO; GO:0019222; P:regulation of metabolic process; IMP:SGD.
DR GO; GO:0006417; P:regulation of translation; IMP:SGD.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:SGD.
DR GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR GO; GO:0002127; P:tRNA wobble base cytosine methylation; IMP:SGD.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR023270; RCMT_NCL1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22808; PTHR22808; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR PRINTS; PR02011; RCMTNCL1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding; S-adenosyl-L-methionine; Transferase; tRNA processing;
KW tRNA-binding.
FT CHAIN 1..684
FT /note="Multisite-specific tRNA:(cytosine-C(5))-
FT methyltransferase"
FT /id="PRO_0000211820"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 650..684
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 652..667
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 668..684
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 310
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 173..179
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 202
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 229
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 257
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT MOD_RES 426
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 431
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 667
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
SQ SEQUENCE 684 AA; 77879 MW; 92FA9177CF4AB2CF CRC64;
MARRKNFKKG NKKTFGARDD SRAQKNWSEL VKENEKWEKY YKTLALFPED QWEEFKKTCQ
APLPLTFRIT GSRKHAGEVL NLFKERHLPN LTNVEFEGEK IKAPVELPWY PDHLAWQLDV
PKTVIRKNEQ FAKTQRFLVV ENAVGNISRQ EAVSMIPPIV LEVKPHHTVL DMCAAPGSKT
AQLIEALHKD TDEPSGFVVA NDADARRSHM LVHQLKRLNS ANLMVVNHDA QFFPRIRLHG
NSNNKNDVLK FDRILCDVPC SGDGTMRKNV NVWKDWNTQA GLGLHAVQLN ILNRGLHLLK
NNGRLVYSTC SLNPIENEAV VAEALRKWGD KIRLVNCDDK LPGLIRSKGV SKWPVYDRNL
TEKTKGDEGT LDSFFSPSEE EASKFNLQNC MRVYPHQQNT GGFFITVFEK VEDSTEAATE
KLSSETPALE SEGPQTKKIK VEEVQKKERL PRDANEEPFV FVDPQHEALK VCWDFYGIDN
IFDRNTCLVR NATGEPTRVV YTVCPALKDV IQANDDRLKI IYSGVKLFVS QRSDIECSWR
IQSESLPIMK HHMKSNRIVE ANLEMLKHLL IESFPNFDDI RSKNIDNDFV EKMTKLSSGC
AFIDVSRNDP AKENLFLPVW KGNKCINLMV CKEDTHELLY RIFGIDANAK ATPSAEEKEK
EKETTESPAE TTTGTSTEAP SAAN
