Reviewed, UniProtKB/Swiss-Prot P38205 (NCL1_YEAST)

Names and origin

Protein names

Recommended name:
    tRNA (cytosine-5-)-methyltransferase NCL1
    EC=2.1.1.29
Alternative name(s):
    tRNA methyltransferase 4
    Multisite-specific tRNA:m5C-methyltransferase

Gene names

Name:	NCL1
Synonyms:	TRM4
Ordered Locus Names:	YBL024W
ORF Names:	YBL0437

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	684 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. Ref.3 Ref.4
Catalytic activity	S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine.
Subcellular location	Nucleus › nucleolus. Ref.3
Miscellaneous	Present with 16100 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the methyltransferase superfamily. RsmB/NOP family. TRM4 subfamily.

Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Nucleus
Ligand	RNA-binding S-adenosyl-L-methionine tRNA-binding
Molecular function	Methyltransferase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	tRNA methylation Ref.4 Inferred from direct assay. Source: SGD
Cellular component	nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	tRNA (cytosine-5-)-methyltransferase activity Ref.4 Inferred from direct assay. Source: SGD tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 684	684	tRNA (cytosine-5-)-methyltransferase NCL1		PRO_0000211820
Regions
	Region	173 – 179	7	S-adenosyl-L-methionine binding By similarity
Sites
	Active site	310	1	Nucleophile Potential
	Binding site	202	1	S-adenosyl-L-methionine By similarity
	Binding site	229	1	S-adenosyl-L-methionine By similarity
	Binding site	257	1	S-adenosyl-L-methionine By similarity
Amino acid modifications
	Modified residue	423	1	Phosphoserine Ref.7
	Modified residue	424	1	Phosphoserine Ref.7
	Modified residue	426	1	Phosphothreonine Ref.7
	Modified residue	431	1	Phosphoserine Ref.7
	Modified residue	665	1	Phosphothreonine Ref.6
	Modified residue	667	1	Phosphoserine Ref.6

Sequences

	Sequence		Length	Mass (Da)
	P38205-1 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: 92FA9177CF4AB2CF	FASTA	684	77,879
	10 20 30 40 50 60 MARRKNFKKG NKKTFGARDD SRAQKNWSEL VKENEKWEKY YKTLALFPED QWEEFKKTCQ 70 80 90 100 110 120 APLPLTFRIT GSRKHAGEVL NLFKERHLPN LTNVEFEGEK IKAPVELPWY PDHLAWQLDV 130 140 150 160 170 180 PKTVIRKNEQ FAKTQRFLVV ENAVGNISRQ EAVSMIPPIV LEVKPHHTVL DMCAAPGSKT 190 200 210 220 230 240 AQLIEALHKD TDEPSGFVVA NDADARRSHM LVHQLKRLNS ANLMVVNHDA QFFPRIRLHG 250 260 270 280 290 300 NSNNKNDVLK FDRILCDVPC SGDGTMRKNV NVWKDWNTQA GLGLHAVQLN ILNRGLHLLK 310 320 330 340 350 360 NNGRLVYSTC SLNPIENEAV VAEALRKWGD KIRLVNCDDK LPGLIRSKGV SKWPVYDRNL 370 380 390 400 410 420 TEKTKGDEGT LDSFFSPSEE EASKFNLQNC MRVYPHQQNT GGFFITVFEK VEDSTEAATE 430 440 450 460 470 480 KLSSETPALE SEGPQTKKIK VEEVQKKERL PRDANEEPFV FVDPQHEALK VCWDFYGIDN 490 500 510 520 530 540 IFDRNTCLVR NATGEPTRVV YTVCPALKDV IQANDDRLKI IYSGVKLFVS QRSDIECSWR 550 560 570 580 590 600 IQSESLPIMK HHMKSNRIVE ANLEMLKHLL IESFPNFDDI RSKNIDNDFV EKMTKLSSGC 610 620 630 640 650 660 AFIDVSRNDP AKENLFLPVW KGNKCINLMV CKEDTHELLY RIFGIDANAK ATPSAEEKEK 670 680 EKETTESPAE TTTGTSTEAP SAAN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the ribosomal protein L19 as well as proteins with homologies to components of the hnRNP and snRNP complexes and to the human proliferation-associated p120 antigen." van Dyck L., Jonniaux J.-L., Barreiros T.D.M., Kleine K., Goffeau A. Yeast 10:1663-1673(1994) [PubMed: 7725803] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed: 7813418] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces cerevisiae." Wu P., Brockenbrough J.S., Paddy M.R., Aris J.P. Gene 220:109-117(1998) [PubMed: 9767141] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[4]	"Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme." Motorin Y., Grosjean H. RNA 5:1105-1118(1999) [PubMed: 10445884] [Abstract] Cited for: FUNCTION.
[5]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-665 AND SER-667, MASS SPECTROMETRY.
[7]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-423; SER-424; THR-426 AND SER-431, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X77291 Genomic DNA. Translation: CAA54502.1. Z35785 Genomic DNA. Translation: CAA84843.1.
PIR	S45758.
RefSeq	NP_009529.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:3932N.
IntAct	P38205. 22 interactions.
STRING	P38205.
Proteomic databases
PeptideAtlas	P38205.
Genome annotation databases
Ensembl	YBL024W; YBL024W; YBL024W; Saccharomyces cerevisiae. [Genome view]
GeneID	852257.
GenomeReviews	Gene locus YBL024W in contig Y13134_GR.
KEGG	sce:YBL024W.
NMPDR	fig|4932.3.peg.222.
Organism-specific databases
CYGD	YBL024w.
SGD	S000000120. NCL1.
Phylogenomic databases
HOGENOM	P38205.
OMA	QTKRMCT.
Enzyme and pathway databases
BRENDA	2.1.1.29. 250.
Gene expression databases
ArrayExpress	P38205.
Genevestigator	P38205.
GermOnline	YBL024W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR001678. Fmu/NOL1/Nop2p. IPR018314. Fmu/NOL1/Nop2p_CS. [Graphical view]
Pfam	PF01189. Nol1_Nop2_Fmu. 2 hits. [Graphical view]
PROSITE	PS01153. NOL1_NOP2_SUN. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	970841.

Entry information

Entry name

NCL1_YEAST

Accession

Primary (citable) accession number: P38205

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	November 3, 2009
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)