CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-006875
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Multisite-specific tRNA:(cytosine-C(5))-methyltransferase 
Protein Synonyms/Alias
 Multisite-specific tRNA:m5C-methyltransferase; tRNA (cytosine-5-)-methyltransferase NCL1; tRNA methyltransferase 4 
Gene Name
 NCL1 
Gene Synonyms/Alias
 TRM4; YBL024W; YBL0437 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
25RDDSRAQKNWSELVKacetylation[1]
84GEVLNLFKERHLPNLacetylation[1]
245LHGNSNNKNDVLKFDacetylation[1]
250NNKNDVLKFDRILCDacetylation[1]
268SGDGTMRKNVNVWKDubiquitination[2]
352IRSKGVSKWPVYDRNacetylation[1]
421STEAATEKLSSETPAacetylation[1]
440GPQTKKIKVEEVQKKacetylation[1]
508YTVCPALKDVIQANDubiquitination[2]
Reference
 [1] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919]
 [2] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301] 
Functional Description
 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. 
Sequence Annotation
 REGION 173 179 S-adenosyl-L-methionine binding (By
 ACT_SITE 310 310 Nucleophile (Potential).
 BINDING 202 202 S-adenosyl-L-methionine (By similarity).
 BINDING 229 229 S-adenosyl-L-methionine (By similarity).
 BINDING 257 257 S-adenosyl-L-methionine (By similarity).
 MOD_RES 426 426 Phosphothreonine.
 MOD_RES 431 431 Phosphoserine.
 MOD_RES 667 667 Phosphoserine.  
Keyword
 Complete proteome; Methyltransferase; Nucleus; Phosphoprotein; Reference proteome; RNA-binding; S-adenosyl-L-methionine; Transferase; tRNA processing; tRNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 684 AA 
Protein Sequence
MARRKNFKKG NKKTFGARDD SRAQKNWSEL VKENEKWEKY YKTLALFPED QWEEFKKTCQ 60
APLPLTFRIT GSRKHAGEVL NLFKERHLPN LTNVEFEGEK IKAPVELPWY PDHLAWQLDV 120
PKTVIRKNEQ FAKTQRFLVV ENAVGNISRQ EAVSMIPPIV LEVKPHHTVL DMCAAPGSKT 180
AQLIEALHKD TDEPSGFVVA NDADARRSHM LVHQLKRLNS ANLMVVNHDA QFFPRIRLHG 240
NSNNKNDVLK FDRILCDVPC SGDGTMRKNV NVWKDWNTQA GLGLHAVQLN ILNRGLHLLK 300
NNGRLVYSTC SLNPIENEAV VAEALRKWGD KIRLVNCDDK LPGLIRSKGV SKWPVYDRNL 360
TEKTKGDEGT LDSFFSPSEE EASKFNLQNC MRVYPHQQNT GGFFITVFEK VEDSTEAATE 420
KLSSETPALE SEGPQTKKIK VEEVQKKERL PRDANEEPFV FVDPQHEALK VCWDFYGIDN 480
IFDRNTCLVR NATGEPTRVV YTVCPALKDV IQANDDRLKI IYSGVKLFVS QRSDIECSWR 540
IQSESLPIMK HHMKSNRIVE ANLEMLKHLL IESFPNFDDI RSKNIDNDFV EKMTKLSSGC 600
AFIDVSRNDP AKENLFLPVW KGNKCINLMV CKEDTHELLY RIFGIDANAK ATPSAEEKEK 660
EKETTESPAE TTTGTSTEAP SAAN 684 
Gene Ontology
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; IDA:SGD.
 GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IDA:SGD.
 GO:0000049; F:tRNA binding; IEA:UniProtKB-KW. 
Interpro
 IPR001678; Fmu/NOL1/Nop2p.
 IPR018314; Fmu/NOL1/Nop2p_CS.
 IPR023267; RCMT.
 IPR023270; RCMT_NCL1. 
Pfam
 PF01189; Nol1_Nop2_Fmu 
SMART
  
PROSITE
 PS01153; NOL1_NOP2_SUN 
PRINTS
 PR02008; RCMTFAMILY.
 PR02011; RCMTNCL1.