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Protein

60S ribosomal protein L12-A

Gene

RPL12A

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

This protein binds directly to 26S ribosomal RNA.

GO - Molecular functioni

  • RNA binding Source: UniProtKB-KW
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • ribosomal large subunit assembly Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30172-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L12-A
Alternative name(s):
L15
YL23
Gene namesi
Name:RPL12A
Synonyms:RPL15B
Ordered Locus Names:YEL054C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome V

Organism-specific databases

CYGDiYEL054c.
SGDiS000000780. RPL12A.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi67 – 671R → K: Abolishes monomethylation by RMT2. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 16516460S ribosomal protein L12-APRO_0000104467Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N,N-dimethylproline; by NTM12 Publications
Modified residuei4 – 41N6,N6,N6-trimethyllysine; by RKM22 Publications
Modified residuei11 – 111N6,N6,N6-trimethyllysine; by RKM21 Publication
Modified residuei25 – 251Phosphoserine1 Publication
Modified residuei38 – 381Phosphoserine2 Publications
Modified residuei67 – 671N5-methylarginine; by RMT22 Publications

Post-translational modificationi

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.4 Publications

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

MaxQBiP0CX53.
PRIDEiP0CX53.

Expressioni

Gene expression databases

ExpressionAtlasiP0CX53. differential.

Interactioni

Subunit structurei

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).1 Publication

Protein-protein interaction databases

BioGridi32476. 93 interactions.
36675. 88 interactions.
IntActiP0CX53. 1 interaction.
MINTiMINT-8285568.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-K13-143[»]
3J16electron microscopy-H1-165[»]
3J77electron microscopy6.20621-165[»]
3J78electron microscopy6.30621-165[»]
4V4Belectron microscopy11.70BK13-143[»]
4V6Ielectron microscopy8.80BJ1-165[»]
4V7Felectron microscopy8.70I1-165[»]
4V7RX-ray4.00DL1-165[»]
ProteinModelPortaliP0CX53.
SMRiP0CX53. Positions 2-80.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0CX53.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L11P family.Curated

Phylogenomic databases

HOGENOMiHOG000082125.
InParanoidiP0CX53.
KOiK02870.
OrthoDBiEOG71VT57.

Family and domain databases

Gene3Di1.10.10.250. 1 hit.
3.30.1550.10. 1 hit.
HAMAPiMF_00736. Ribosomal_L11.
InterProiIPR000911. Ribosomal_L11/L12.
IPR020783. Ribosomal_L11_C.
IPR020785. Ribosomal_L11_CS.
IPR020784. Ribosomal_L11_N.
[Graphical view]
PANTHERiPTHR11661. PTHR11661. 1 hit.
PfamiPF00298. Ribosomal_L11. 1 hit.
PF03946. Ribosomal_L11_N. 1 hit.
[Graphical view]
SMARTiSM00649. RL11. 1 hit.
[Graphical view]
SUPFAMiSSF46906. SSF46906. 1 hit.
SSF54747. SSF54747. 1 hit.
PROSITEiPS00359. RIBOSOMAL_L11. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0CX53-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPPKFDPNEV KYLYLRAVGG EVGASAALAP KIGPLGLSPK KVGEDIAKAT
60 70 80 90 100
KEFKGIKVTV QLKIQNRQAA ASVVPSASSL VITALKEPPR DRKKDKNVKH
110 120 130 140 150
SGNIQLDEII EIARQMRDKS FGRTLASVTK EILGTAQSVG CRVDFKNPHD
160
IIEGINAGEI EIPEN
Length:165
Mass (Da):17,823
Last modified:June 28, 2011 - v1
Checksum:i0B23A483781DFBE5
GO

Mass spectrometryi

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.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X51519 Genomic DNA. Translation: CAA35891.1.
U18795 Genomic DNA. Translation: AAB65033.1.
AY693201 Genomic DNA. Translation: AAT93220.1.
BK006939 Genomic DNA. Translation: DAA07600.1.
PIRiS13665.
RefSeqiNP_010706.3. NM_001180726.3.
NP_010860.1. NM_001178869.1.

Genome annotation databases

EnsemblFungiiYDR418W; YDR418W; YDR418W.
YEL054C; YEL054C; YEL054C.
GeneIDi852026.
856656.
KEGGisce:YDR418W.
sce:YEL054C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X51519 Genomic DNA. Translation: CAA35891.1.
U18795 Genomic DNA. Translation: AAB65033.1.
AY693201 Genomic DNA. Translation: AAT93220.1.
BK006939 Genomic DNA. Translation: DAA07600.1.
PIRiS13665.
RefSeqiNP_010706.3. NM_001180726.3.
NP_010860.1. NM_001178869.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-K13-143[»]
3J16electron microscopy-H1-165[»]
3J77electron microscopy6.20621-165[»]
3J78electron microscopy6.30621-165[»]
4V4Belectron microscopy11.70BK13-143[»]
4V6Ielectron microscopy8.80BJ1-165[»]
4V7Felectron microscopy8.70I1-165[»]
4V7RX-ray4.00DL1-165[»]
ProteinModelPortaliP0CX53.
SMRiP0CX53. Positions 2-80.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32476. 93 interactions.
36675. 88 interactions.
IntActiP0CX53. 1 interaction.
MINTiMINT-8285568.

Proteomic databases

MaxQBiP0CX53.
PRIDEiP0CX53.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR418W; YDR418W; YDR418W.
YEL054C; YEL054C; YEL054C.
GeneIDi852026.
856656.
KEGGisce:YDR418W.
sce:YEL054C.

Organism-specific databases

CYGDiYEL054c.
SGDiS000000780. RPL12A.

Phylogenomic databases

HOGENOMiHOG000082125.
InParanoidiP0CX53.
KOiK02870.
OrthoDBiEOG71VT57.

Enzyme and pathway databases

BioCyciYEAST:G3O-30172-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.

Miscellaneous databases

EvolutionaryTraceiP0CX53.
NextBioi970252.
PROiP0CX53.

Gene expression databases

ExpressionAtlasiP0CX53. differential.

Family and domain databases

Gene3Di1.10.10.250. 1 hit.
3.30.1550.10. 1 hit.
HAMAPiMF_00736. Ribosomal_L11.
InterProiIPR000911. Ribosomal_L11/L12.
IPR020783. Ribosomal_L11_C.
IPR020785. Ribosomal_L11_CS.
IPR020784. Ribosomal_L11_N.
[Graphical view]
PANTHERiPTHR11661. PTHR11661. 1 hit.
PfamiPF00298. Ribosomal_L11. 1 hit.
PF03946. Ribosomal_L11_N. 1 hit.
[Graphical view]
SMARTiSM00649. RL11. 1 hit.
[Graphical view]
SUPFAMiSSF46906. SSF46906. 1 hit.
SSF54747. SSF54747. 1 hit.
PROSITEiPS00359. RIBOSOMAL_L11. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. 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, METHYLATION AT LYS-11 BY RKM2, 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  11. 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 AND ARG-67, METHYLATION AT LYS-4 BY RKM2.
  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.

Entry informationi

Entry nameiRL12A_YEAST
AccessioniPrimary (citable) accession number: P0CX53
Secondary accession number(s): D3DLJ6, P05741, P17079
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: June 28, 2011
Last modified: July 22, 2015
This is version 39 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 68500 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for L12 in yeast.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

External Data

Dasty 3

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 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.