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Protein

Multisite-specific tRNA:(cytosine-C(5))-methyltransferase

Gene

NCL1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Methylates cytosine to m5C at several positions in different tRNAs and pre-tRNAs containing intron. Able to modify tRNAs at all four positions (34, 40, 48 and 49) at which m5C has been found in tRNAs. May be involved in ribosome biogenesis as its disruption leads to increased sensitivity to the antibiotic paromomycin.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + cytosine(34) in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine(34) in tRNA precursor.1 Publication
S-adenosyl-L-methionine + cytosine(40) in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine(40) in tRNA precursor.1 Publication
S-adenosyl-L-methionine + cytosine(48) in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(48) in tRNA.1 Publication
S-adenosyl-L-methionine + cytosine(49) in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(49) in tRNA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei202S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei229S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei257S-adenosyl-L-methioninePROSITE-ProRule annotation1
Active sitei310NucleophilePROSITE-ProRule annotation1

GO - Molecular functioni

  • tRNA (cytosine-5-)-methyltransferase activity Source: SGD
  • tRNA binding Source: SGD

GO - Biological processi

  • cellular response to hydrogen peroxide Source: SGD
  • tRNA methylation Source: SGD
  • tRNA modification Source: Reactome
  • wobble base cytosine methylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine, tRNA-binding

Enzyme and pathway databases

BioCyciMetaCyc:G3O-28927-MONOMER.
YEAST:G3O-28927-MONOMER.
BRENDAi2.1.1.202. 984.
ReactomeiR-SCE-6782315. tRNA modification in the nucleus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
Multisite-specific tRNA:(cytosine-C(5))-methyltransferase (EC:2.1.1.202)
Alternative name(s):
Multisite-specific tRNA:m5C-methyltransferase
tRNA (cytosine-5-)-methyltransferase NCL1
tRNA methyltransferase 4
Gene namesi
Name:NCL1
Synonyms:TRM4
Ordered Locus Names:YBL024W
ORF Names:YBL0437
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBL024W.
SGDiS000000120. NCL1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: GO_Central
  • nucleolus Source: UniProtKB-SubCell
  • nucleoplasm Source: Reactome
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002118201 – 684Multisite-specific tRNA:(cytosine-C(5))-methyltransferaseAdd BLAST684

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei426PhosphothreonineCombined sources1
Modified residuei431PhosphoserineCombined sources1
Modified residuei667PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38205.
PRIDEiP38205.

PTM databases

iPTMnetiP38205.

Interactioni

Protein-protein interaction databases

BioGridi32674. 98 interactors.
DIPiDIP-3932N.
IntActiP38205. 22 interactors.
MINTiMINT-503175.

Structurei

3D structure databases

ProteinModelPortaliP38205.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni173 – 179S-adenosyl-L-methionine bindingPROSITE-ProRule annotation7

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. TRM4 subfamily.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00660000095589.
HOGENOMiHOG000205147.
InParanoidiP38205.
KOiK15334.
OMAiINSSAQC.
OrthoDBiEOG092C4JQ0.

Family and domain databases

Gene3Di3.40.50.150. 2 hits.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR001678. MeTrfase_RsmB/NOP2.
IPR023267. RCMT.
IPR023270. RCMT_NCL1.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
PR02011. RCMTNCL1.
SUPFAMiSSF53335. SSF53335. 2 hits.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38205-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARRKNFKKG NKKTFGARDD SRAQKNWSEL VKENEKWEKY YKTLALFPED
60 70 80 90 100
QWEEFKKTCQ APLPLTFRIT GSRKHAGEVL NLFKERHLPN LTNVEFEGEK
110 120 130 140 150
IKAPVELPWY PDHLAWQLDV PKTVIRKNEQ FAKTQRFLVV ENAVGNISRQ
160 170 180 190 200
EAVSMIPPIV LEVKPHHTVL DMCAAPGSKT AQLIEALHKD TDEPSGFVVA
210 220 230 240 250
NDADARRSHM LVHQLKRLNS ANLMVVNHDA QFFPRIRLHG NSNNKNDVLK
260 270 280 290 300
FDRILCDVPC SGDGTMRKNV NVWKDWNTQA GLGLHAVQLN ILNRGLHLLK
310 320 330 340 350
NNGRLVYSTC SLNPIENEAV VAEALRKWGD KIRLVNCDDK LPGLIRSKGV
360 370 380 390 400
SKWPVYDRNL TEKTKGDEGT LDSFFSPSEE EASKFNLQNC MRVYPHQQNT
410 420 430 440 450
GGFFITVFEK VEDSTEAATE KLSSETPALE SEGPQTKKIK VEEVQKKERL
460 470 480 490 500
PRDANEEPFV FVDPQHEALK VCWDFYGIDN IFDRNTCLVR NATGEPTRVV
510 520 530 540 550
YTVCPALKDV IQANDDRLKI IYSGVKLFVS QRSDIECSWR IQSESLPIMK
560 570 580 590 600
HHMKSNRIVE ANLEMLKHLL IESFPNFDDI RSKNIDNDFV EKMTKLSSGC
610 620 630 640 650
AFIDVSRNDP AKENLFLPVW KGNKCINLMV CKEDTHELLY RIFGIDANAK
660 670 680
ATPSAEEKEK EKETTESPAE TTTGTSTEAP SAAN
Length:684
Mass (Da):77,879
Last modified:October 1, 1994 - v1
Checksum:i92FA9177CF4AB2CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77291 Genomic DNA. Translation: CAA54502.1.
Z35785 Genomic DNA. Translation: CAA84843.1.
BK006936 Genomic DNA. Translation: DAA07096.1.
PIRiS45758.
RefSeqiNP_009529.1. NM_001178264.1.

Genome annotation databases

EnsemblFungiiYBL024W; YBL024W; YBL024W.
GeneIDi852257.
KEGGisce:YBL024W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77291 Genomic DNA. Translation: CAA54502.1.
Z35785 Genomic DNA. Translation: CAA84843.1.
BK006936 Genomic DNA. Translation: DAA07096.1.
PIRiS45758.
RefSeqiNP_009529.1. NM_001178264.1.

3D structure databases

ProteinModelPortaliP38205.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32674. 98 interactors.
DIPiDIP-3932N.
IntActiP38205. 22 interactors.
MINTiMINT-503175.

PTM databases

iPTMnetiP38205.

Proteomic databases

MaxQBiP38205.
PRIDEiP38205.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBL024W; YBL024W; YBL024W.
GeneIDi852257.
KEGGisce:YBL024W.

Organism-specific databases

EuPathDBiFungiDB:YBL024W.
SGDiS000000120. NCL1.

Phylogenomic databases

GeneTreeiENSGT00660000095589.
HOGENOMiHOG000205147.
InParanoidiP38205.
KOiK15334.
OMAiINSSAQC.
OrthoDBiEOG092C4JQ0.

Enzyme and pathway databases

BioCyciMetaCyc:G3O-28927-MONOMER.
YEAST:G3O-28927-MONOMER.
BRENDAi2.1.1.202. 984.
ReactomeiR-SCE-6782315. tRNA modification in the nucleus and cytosol.

Miscellaneous databases

PROiP38205.

Family and domain databases

Gene3Di3.40.50.150. 2 hits.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR001678. MeTrfase_RsmB/NOP2.
IPR023267. RCMT.
IPR023270. RCMT_NCL1.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
PR02011. RCMTNCL1.
SUPFAMiSSF53335. SSF53335. 2 hits.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNCL1_YEAST
AccessioniPrimary (citable) accession number: P38205
Secondary accession number(s): D6VPX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 2, 2016
This is version 137 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 16100 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.