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P0CX53 (RL12A_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 27. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
60S ribosomal protein L12-A
Alternative name(s):
L15
YL23
Gene names
Name:RPL12A
Synonyms:RPL15B
Ordered Locus Names:YEL054C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length165 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

This protein binds directly to 26S ribosomal RNA. HAMAP-Rule MF_00736

Subunit structure

Component of the large ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains 32 different proteins (encoded by 56 genes) and 1 molecule of RNA (18S). The 60S subunit contains 46 different proteins (encoded by 81 genes) and 3 molecules of RNA (25S, 5.8S and 5S). Ref.7

Subcellular location

Cytoplasm Ref.10.

Post-translational modification

It appears that the main modified species for L12 contains 6 methyl groups, 2 on Pro-2, 3 on Lys-4 and 1 on Arg-67. Although not reproduced with a second method, methylation at Lys-11 cannot be ruled out. HAMAP-Rule MF_00736

Miscellaneous

Present with 68500 molecules/cell in log phase SD medium.

There are 2 genes for L12 in yeast.

Sequence similarities

Belongs to the ribosomal protein L11P family.

Mass spectrometry

Molecular mass is 17764.712 Da from positions 2 - 106. Determined by ESI. Monoisotopic mass with either 6 methylation modifications or 1 acetylation and 3 methylation modifications. Ref.9

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.5
Chain2 – 16516460S ribosomal protein L12-A HAMAP-Rule MF_00736
PRO_0000104467

Amino acid modifications

Modified residue21N,N-dimethylproline; by NTM1 Ref.12 Ref.15
Modified residue41N6,N6,N6-trimethyllysine; by RKM2 Ref.5 Ref.12
Modified residue111N6,N6,N6-trimethyllysine; by RKM2 Ref.5
Modified residue251Phosphoserine Ref.14
Modified residue381Phosphoserine Ref.13 Ref.14
Modified residue671N5-methylarginine; by RMT2 Ref.8 Ref.12

Experimental info

Mutagenesis671R → K: Abolishes monomethylation by RMT2. Ref.8

Sequences

Sequence LengthMass (Da)Tools
P0CX53 [UniParc].

Last modified June 28, 2011. Version 1.
Checksum: 0B23A483781DFBE5

FASTA16517,823
        10         20         30         40         50         60 
MPPKFDPNEV KYLYLRAVGG EVGASAALAP KIGPLGLSPK KVGEDIAKAT KEFKGIKVTV 

        70         80         90        100        110        120 
QLKIQNRQAA ASVVPSASSL VITALKEPPR DRKKDKNVKH SGNIQLDEII EIARQMRDKS 

       130        140        150        160 
FGRTLASVTK EILGTAQSVG CRVDFKNPHD IIEGINAGEI EIPEN 

« Hide

References

« Hide 'large scale' references
[1]"The 26S rRNA binding ribosomal protein equivalent to bacterial protein L11 is encoded by unspliced duplicated genes in Saccharomyces cerevisiae."
Pucciarelli G., Remacha M., Ballesta J.P.G.
Nucleic Acids Res. 18:4409-4416(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: Y166.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome V."
Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. expand/collapse author list , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.
Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"A novel SET domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10."
Porras-Yakushi T.R., Whitelegge J.P., Clarke S.
J. Biol. Chem. 281:35835-35845(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-16, METHYLATION AT LYS-4 AND LYS-11, IDENTIFICATION BY MASS SPECTROMETRY.
[6]"Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence characterization of twenty-four proteins from cytoplasmic ribosomes."
Otaka E., Higo K., Itoh T.
Mol. Gen. Genet. 195:544-546(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL PROTEIN SEQUENCE OF 17-36.
[7]"The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
Planta R.J., Mager W.H.
Yeast 14:471-477(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NOMENCLATURE, SUBUNIT.
[8]"Yeast ribosomal protein L12 is a substrate of protein-arginine methyltransferase 2."
Chern M.-K., Chang K.-N., Liu L.-F., Tam T.-C.S., Liu Y.-C., Liang Y.-L., Tam M.F.
J. Biol. Chem. 277:15345-15353(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, METHYLATION AT ARG-67, MUTAGENESIS OF ARG-67.
[9]"Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR."
Lee S.-W., Berger S.J., Martinovic S., Pasa-Tolic L., Anderson G.A., Shen Y., Zhao R., Smith R.D.
Proc. Natl. Acad. Sci. U.S.A. 99:5942-5947(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY.
[10]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]"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] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]"Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab."
Webb K.J., Laganowsky A., Whitelegge J.P., Clarke S.G.
J. Biol. Chem. 283:35561-35568(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: METHYLATION AT PRO-2; LYS-4 AND ARG-67.
[13]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-25 AND SER-38, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Identification of protein N-terminal methyltransferases in yeast and humans."
Webb K.J., Lipson R.S., Al-Hadid Q., Whitelegge J.P., Clarke S.G.
Biochemistry 49:5225-5235(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: METHYLATION AT PRO-2 BY NTM1/TAE1.
[16]"Sites of ubiquitin attachment in Saccharomyces cerevisiae."
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[17]"Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions."
Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J.
Cell 107:373-386(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING OF 13-143, ELECTRON MICROSCOPY.
[18]"Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation."
Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J.
EMBO J. 23:1008-1019(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING OF 13-143, ELECTRON MICROSCOPY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X51519 Genomic DNA. Translation: CAA35891.1.
U18795 Genomic DNA. Translation: AAB65033.1.
AY693201 Genomic DNA. Translation: AAT93220.1.
BK006939 Genomic DNA. Translation: DAA07600.1.
PIRS13665.
RefSeqNP_010706.3. NM_001180726.3.
NP_010860.1. NM_001178869.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-K13-143[»]
1S1Ielectron microscopy11.70K13-143[»]
3IZSelectron microscopy-J1-165[»]
3J16electron microscopy-H1-165[»]
3J65electron microscopy8.70I1-165[»]
3O5HX-ray4.00L1-165[»]
ProteinModelPortalP0CX53.
SMRP0CX53. Positions 7-144.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32476. 91 interactions.
36675. 86 interactions.
IntActP0CX53. 1 interaction.
MINTMINT-8285568.

Proteomic databases

MaxQBP0CX53.
PRIDEP0CX53.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDR418W; YDR418W; YDR418W.
YEL054C; YEL054C; YEL054C.
GeneID852026.
856656.
KEGGsce:YDR418W.
sce:YEL054C.

Organism-specific databases

CYGDYEL054c.
SGDS000000780. RPL12A.

Phylogenomic databases

HOGENOMHOG000082125.
KOK02870.
OrthoDBEOG71VT57.

Enzyme and pathway databases

BioCycYEAST:G3O-30172-MONOMER.

Family and domain databases

Gene3D1.10.10.250. 1 hit.
3.30.1550.10. 1 hit.
HAMAPMF_00736. Ribosomal_L11.
InterProIPR000911. Ribosomal_L11/L12.
IPR020783. Ribosomal_L11_C.
IPR020785. Ribosomal_L11_CS.
IPR020784. Ribosomal_L11_N.
[Graphical view]
PANTHERPTHR11661. PTHR11661. 1 hit.
PfamPF00298. Ribosomal_L11. 1 hit.
PF03946. Ribosomal_L11_N. 1 hit.
[Graphical view]
SMARTSM00649. RL11. 1 hit.
[Graphical view]
SUPFAMSSF46906. SSF46906. 1 hit.
SSF54747. SSF54747. 1 hit.
PROSITEPS00359. RIBOSOMAL_L11. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0CX53.
NextBio970252.

Entry information

Entry nameRL12A_YEAST
AccessionPrimary (citable) accession number: P0CX53
Secondary accession number(s): D3DLJ6, P05741, P17079
Entry history
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: June 28, 2011
Last modified: May 14, 2014
This is version 27 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome V

Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references