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Protein

60S ribosomal protein L42-A

Gene

RPL42A

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

GO - Molecular functioni

  1. structural constituent of ribosome Source: SGD

GO - Biological processi

  1. cytoplasmic translation Source: SGD
  2. response to antibiotic Source: UniProtKB-KW
  3. response to cycloheximide Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Biological processi

Antibiotic resistance, Cycloheximide resistance

Enzyme and pathway databases

BioCyciYEAST:G3O-33178-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 L42-A
Alternative name(s):
L41
YL27
YP44
Gene namesi
Name:RPL42A
Synonyms:RPL41A, SCL41A
Ordered Locus Names:YNL162W
ORF Names:N1722
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIV

Organism-specific databases

CYGDiYNL162w.
SGDiS000005106. RPL42A.

Subcellular locationi

  1. Cytoplasm 1 Publication

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 10610560S ribosomal protein L42-APRO_0000149147Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei40 – 401N6-methyllysine; by RKM33 Publications
Modified residuei55 – 551N6-methyllysine; by RKM42 Publications

Post-translational modificationi

In wild-type cells, 78% of L42 is monomethylated at both Lys-40 and Lys-55, and 22% are a mixture of species with either residue monomethylated.

Keywords - PTMi

Methylation

Proteomic databases

MaxQBiP0CX27.

Expressioni

Gene expression databases

ExpressionAtlasiP0CX27. 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

BioGridi35667. 30 interactions.
36574. 64 interactions.
MINTiMINT-2782780.

Structurei

Secondary structure

1
106
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 127Combined sources
Turni15 – 173Combined sources
Beta strandi19 – 279Combined sources
Helixi38 – 4710Combined sources
Beta strandi48 – 525Combined sources
Beta strandi66 – 749Combined sources
Turni75 – 773Combined sources
Beta strandi80 – 9011Combined sources
Beta strandi92 – 943Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-12-92[»]
3J6Xelectron microscopy6.10821-106[»]
3J6Yelectron microscopy6.10821-106[»]
3J77electron microscopy6.20921-106[»]
3J78electron microscopy6.30921-106[»]
4U3MX-ray3.00Q2/q22-106[»]
4U3NX-ray3.20Q2/q22-106[»]
4U3UX-ray2.90Q2/q22-106[»]
4U4NX-ray3.10Q2/q22-106[»]
4U4OX-ray3.60Q2/q22-106[»]
4U4QX-ray3.00Q2/q22-106[»]
4U4RX-ray2.80Q2/q22-106[»]
4U4UX-ray3.00Q2/q22-106[»]
4U4YX-ray3.20Q2/q22-106[»]
4U4ZX-ray3.10Q2/q22-106[»]
4U50X-ray3.20Q2/q22-106[»]
4U51X-ray3.20Q2/q22-106[»]
4U52X-ray3.00Q2/q22-106[»]
4U53X-ray3.30Q2/q22-106[»]
4U55X-ray3.20Q2/q22-106[»]
4U56X-ray3.45Q2/q22-106[»]
4U6FX-ray3.10Q2/q22-106[»]
4V4Belectron microscopy11.70BZ2-106[»]
4V6Ielectron microscopy8.80Br1-106[»]
4V7RX-ray4.00Bf/Df1-106[»]
4V88X-ray3.00Bo/Do1-106[»]
4V8Telectron microscopy8.10o1-106[»]
4V8Yelectron microscopy4.30Bo2-106[»]
4V8Zelectron microscopy6.60Bo2-106[»]
4V91electron microscopy3.70o1-106[»]
ProteinModelPortaliP0CX27.
SMRiP0CX27. Positions 2-106.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0CX27.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L44e family.Curated

Phylogenomic databases

HOGENOMiHOG000224989.
InParanoidiP0CX27.
KOiK02929.
OrthoDBiEOG7MWH8Z.

Family and domain databases

Gene3Di3.10.450.80. 1 hit.
InterProiIPR000552. Ribosomal_L44e.
IPR011332. Ribosomal_zn-bd.
[Graphical view]
PANTHERiPTHR10369. PTHR10369. 1 hit.
PfamiPF00935. Ribosomal_L44. 1 hit.
[Graphical view]
ProDomiPD002841. Ribosomal_L44e. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF57829. SSF57829. 1 hit.
PROSITEiPS01172. RIBOSOMAL_L44E. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P0CX27-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVNVPKTRKT YCKGKTCRKH TQHKVTQYKA GKASLFAQGK RRYDRKQSGF
60 70 80 90 100
GGQTKPVFHK KAKTTKKVVL RLECVKCKTR AQLTLKRCKH FELGGEKKQK

GQALQF
Length:106
Mass (Da):12,212
Last modified:June 28, 2011 - v1
Checksum:i730CA11F2CF7F2B4
GO

Sequence cautioni

The sequence CAA96049.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti40 – 412KR → RK AA sequence (PubMed:365584).Curated
Sequence conflicti88 – 892Missing AA sequence (PubMed:365584).Curated

Mass spectrometryi

Molecular mass is 12100.729 Da from positions 2 - 106. Determined by ESI. Monoisotopic mass with 2 methylation modifications.1 Publication
Molecular mass is 12100.71 Da from positions 2 - 106. Determined by ESI. Monoisotopic mass with N6-methyl-Lys-40 and N6-methyl-Lys-55.1 Publication
Molecular mass is 12108.0 Da from positions 2 - 106. Determined by ESI. With N6-methyl-Lys-40 and N6-methyl-Lys-55.1 Publication

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti56 – 561P → Q Confers resistance to cycloheximide, an inhibitor of polypeptide elongation. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10578 Genomic DNA. Translation: BAA01435.1.
X92517 Genomic DNA. Translation: CAA63277.1.
Z71438 Genomic DNA. Translation: CAA96049.1. Sequence problems.
BK006947 Genomic DNA. Translation: DAA10387.1.
PIRiS63114.
RefSeqiNP_012010.1. NM_001179271.1.
NP_014237.2. NM_001183000.1.

Genome annotation databases

EnsemblFungiiYHR141C; YHR141C; YHR141C.
YNL162W; YNL162W; YNL162W.
GeneIDi855560.
856544.
KEGGisce:YHR141C.
sce:YNL162W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10578 Genomic DNA. Translation: BAA01435.1.
X92517 Genomic DNA. Translation: CAA63277.1.
Z71438 Genomic DNA. Translation: CAA96049.1. Sequence problems.
BK006947 Genomic DNA. Translation: DAA10387.1.
PIRiS63114.
RefSeqiNP_012010.1. NM_001179271.1.
NP_014237.2. NM_001183000.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-12-92[»]
3J6Xelectron microscopy6.10821-106[»]
3J6Yelectron microscopy6.10821-106[»]
3J77electron microscopy6.20921-106[»]
3J78electron microscopy6.30921-106[»]
4U3MX-ray3.00Q2/q22-106[»]
4U3NX-ray3.20Q2/q22-106[»]
4U3UX-ray2.90Q2/q22-106[»]
4U4NX-ray3.10Q2/q22-106[»]
4U4OX-ray3.60Q2/q22-106[»]
4U4QX-ray3.00Q2/q22-106[»]
4U4RX-ray2.80Q2/q22-106[»]
4U4UX-ray3.00Q2/q22-106[»]
4U4YX-ray3.20Q2/q22-106[»]
4U4ZX-ray3.10Q2/q22-106[»]
4U50X-ray3.20Q2/q22-106[»]
4U51X-ray3.20Q2/q22-106[»]
4U52X-ray3.00Q2/q22-106[»]
4U53X-ray3.30Q2/q22-106[»]
4U55X-ray3.20Q2/q22-106[»]
4U56X-ray3.45Q2/q22-106[»]
4U6FX-ray3.10Q2/q22-106[»]
4V4Belectron microscopy11.70BZ2-106[»]
4V6Ielectron microscopy8.80Br1-106[»]
4V7RX-ray4.00Bf/Df1-106[»]
4V88X-ray3.00Bo/Do1-106[»]
4V8Telectron microscopy8.10o1-106[»]
4V8Yelectron microscopy4.30Bo2-106[»]
4V8Zelectron microscopy6.60Bo2-106[»]
4V91electron microscopy3.70o1-106[»]
ProteinModelPortaliP0CX27.
SMRiP0CX27. Positions 2-106.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35667. 30 interactions.
36574. 64 interactions.
MINTiMINT-2782780.

Proteomic databases

MaxQBiP0CX27.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYHR141C; YHR141C; YHR141C.
YNL162W; YNL162W; YNL162W.
GeneIDi855560.
856544.
KEGGisce:YHR141C.
sce:YNL162W.

Organism-specific databases

CYGDiYNL162w.
SGDiS000005106. RPL42A.

Phylogenomic databases

HOGENOMiHOG000224989.
InParanoidiP0CX27.
KOiK02929.
OrthoDBiEOG7MWH8Z.

Enzyme and pathway databases

BioCyciYEAST:G3O-33178-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

EvolutionaryTraceiP0CX27.
NextBioi979652.
PROiP0CX27.

Gene expression databases

ExpressionAtlasiP0CX27. differential.

Family and domain databases

Gene3Di3.10.450.80. 1 hit.
InterProiIPR000552. Ribosomal_L44e.
IPR011332. Ribosomal_zn-bd.
[Graphical view]
PANTHERiPTHR10369. PTHR10369. 1 hit.
PfamiPF00935. Ribosomal_L44. 1 hit.
[Graphical view]
ProDomiPD002841. Ribosomal_L44e. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF57829. SSF57829. 1 hit.
PROSITEiPS01172. RIBOSOMAL_L44E. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Drastic alteration of cycloheximide sensitivity by substitution of one amino acid in the L41 ribosomal protein of yeasts."
    Kawai S., Murao S., Mochizuki M., Shibuya I., Yano K., Takagi M.
    J. Bacteriol. 174:254-262(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT GLN-56.
  2. "The sequence of 36.8 kb from the left arm of chromosome XIV reveals 24 complete open reading frames: 18 correspond to new genes, one of which encodes a protein similar to the human myotonic dystrophy kinase."
    Nasr F., Becam A.-M., Herbert C.J.
    Yeast 12:169-175(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "The primary structure of protein 44 from the large subunit of yeast ribosomes."
    Itoh T., Wittmann-Liebold B.
    FEBS Lett. 96:399-402(1978) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-106.
  6. "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.
  7. "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.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "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 LYS-40 AND LYS-55, MASS SPECTROMETRY.
  11. "Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases."
    Couttas T.A., Raftery M.J., Padula M.P., Herbert B.R., Wilkins M.R.
    Proteomics 12:960-972(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION AT LYS-40.
  12. "Stoichiometry of Saccharomyces cerevisiae lysine methylation: insights into non-histone protein lysine methyltransferase activity."
    Hart-Smith G., Chia S.Z., Low J.K., McKay M.J., Molloy M.P., Wilkins M.R.
    J. Proteome Res. 13:1744-1756(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION AT LYS-40 BY RKM3, METHYLATION AT LYS-55 BY RKM4.
  13. "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 2-92, ELECTRON MICROSCOPY.
  14. "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, ELECTRON MICROSCOPY.
  15. "Crystal structure of the eukaryotic ribosome."
    Ben-Shem A., Jenner L., Yusupova G., Yusupov M.
    Science 330:1203-1209(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 80S RIBOSOME.
  16. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.

Entry informationi

Entry nameiRL44A_YEAST
AccessioniPrimary (citable) accession number: P0CX27
Secondary accession number(s): D3DL90, P02405
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: June 28, 2011
Last modified: April 29, 2015
This is version 34 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 13600 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for L42 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.