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P05759

- RS27A_YEAST

UniProt

P05759 - RS27A_YEAST

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Protein
Ubiquitin-40S ribosomal protein S31
Gene
RPS31, RPS37, UBI3, YLR167W, L9470.14
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity.
40S ribosomal protein S31 is a component of the 40S subunit of the ribosome By similarity.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri121 – 14424C4-type
Add
BLAST

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. protein tag Source: SGD
  3. structural constituent of ribosome Source: SGD

GO - Biological processi

  1. cytoplasmic translation Source: SGD
  2. maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) Source: SGD
  3. ribosomal small subunit assembly Source: SGD
  4. ribosome biogenesis Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32297-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-40S ribosomal protein S31
Cleaved into the following 2 chains:
Alternative name(s):
CEP76
S37
YS24
Gene namesi
Name:RPS31
Synonyms:RPS37, UBI3
Ordered Locus Names:YLR167W
ORF Names:L9470.14
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XII

Organism-specific databases

SGDiS000004157. RPS31.

Subcellular locationi

Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytosolic small ribosomal subunit Source: SGD
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi29 – 291K → R: Deficiency in ubiquitin-protein conjugate formation. 2 Publications
Mutagenesisi48 – 481K → R: Deficiency in ubiquitin-protein conjugate formation. 2 Publications
Mutagenesisi63 – 631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676Ubiquitin
PRO_0000396487Add
BLAST
Chaini77 – 1527640S ribosomal protein S31
PRO_0000137688Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei122 – 1221Phosphoserine2 Publications

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP05759.
PaxDbiP05759.
PRIDEiP05759.

2D gel databases

SWISS-2DPAGEP61864.

Expressioni

Gene expression databases

GenevestigatoriP61864.

Interactioni

Subunit structurei

Ribosomal protein S31 is part of the 40S 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

BioGridi31440. 35 interactions.
DIPiDIP-6389N.
IntActiP05759. 16 interactions.
MINTiMINT-8285344.
STRINGi4932.YLR167W.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi79 – 813
Beta strandi106 – 1083
Beta strandi110 – 1123
Turni124 – 1263
Beta strandi128 – 1347
Beta strandi139 – 1468

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VW9electron microscopy6.10g1-152[»]
1VWVelectron microscopy6.10g1-152[»]
3U5CX-ray3.00f1-152[»]
3U5GX-ray3.00f1-152[»]
4BYLelectron microscopy4.3051-152[»]
4BYTelectron microscopy6.6051-152[»]
4CUYelectron microscopy3.70f101-152[»]
ProteinModelPortaliP05759.
SMRiP05759. Positions 1-74, 83-151.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-like
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi77 – 9923Lys-rich (highly basic)
Add
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.
In the C-terminal section; belongs to the ribosomal protein S27Ae family.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5272.
GeneTreeiENSGT00550000074763.
HOGENOMiHOG000224977.
KOiK02977.
OMAiMSILKYY.
OrthoDBiEOG7D5B06.

Family and domain databases

InterProiIPR002906. Ribosomal_S27a.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamiPF01599. Ribosomal_S27. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
SSF57829. SSF57829. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P05759-1 [UniParc]FASTAAdd to Basket

« Hide

MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL    50
EDGRTLSDYN IQKESTLHLV LRLRGGGKKR KKKVYTTPKK IKHKHKKVKL 100
AVLSYYKVDA EGKVTKLRRE CSNPTCGAGV FLANHKDRLY CGKCHSVYKV 150
NA 152
Length:152
Mass (Da):17,216
Last modified:August 10, 2010 - v3
Checksum:i53BF38E2E2F8B38E
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X05730 Genomic DNA. Translation: CAA29197.1.
U17246 Genomic DNA. Translation: AAB67466.1.
BK006945 Genomic DNA. Translation: DAA09489.1.
PIRiC29456. UQBYR7.
RefSeqiNP_013268.1. NM_001182054.1.

Genome annotation databases

EnsemblFungiiYLR167W; YLR167W; YLR167W.
GeneIDi850864.
KEGGisce:YLR167W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X05730 Genomic DNA. Translation: CAA29197.1 .
U17246 Genomic DNA. Translation: AAB67466.1 .
BK006945 Genomic DNA. Translation: DAA09489.1 .
PIRi C29456. UQBYR7.
RefSeqi NP_013268.1. NM_001182054.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1VW9 electron microscopy 6.10 g 1-152 [» ]
1VWV electron microscopy 6.10 g 1-152 [» ]
3U5C X-ray 3.00 f 1-152 [» ]
3U5G X-ray 3.00 f 1-152 [» ]
4BYL electron microscopy 4.30 5 1-152 [» ]
4BYT electron microscopy 6.60 5 1-152 [» ]
4CUY electron microscopy 3.70 f 101-152 [» ]
ProteinModelPortali P05759.
SMRi P05759. Positions 1-74, 83-151.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31440. 35 interactions.
DIPi DIP-6389N.
IntActi P05759. 16 interactions.
MINTi MINT-8285344.
STRINGi 4932.YLR167W.

2D gel databases

SWISS-2DPAGE P61864.

Proteomic databases

MaxQBi P05759.
PaxDbi P05759.
PRIDEi P05759.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YLR167W ; YLR167W ; YLR167W .
GeneIDi 850864.
KEGGi sce:YLR167W.

Organism-specific databases

SGDi S000004157. RPS31.

Phylogenomic databases

eggNOGi COG5272.
GeneTreei ENSGT00550000074763.
HOGENOMi HOG000224977.
KOi K02977.
OMAi MSILKYY.
OrthoDBi EOG7D5B06.

Enzyme and pathway databases

BioCyci YEAST:G3O-32297-MONOMER.

Miscellaneous databases

NextBioi 967191.
PROi P05759.

Gene expression databases

Genevestigatori P61864.

Family and domain databases

InterProi IPR002906. Ribosomal_S27a.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view ]
Pfami PF01599. Ribosomal_S27. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view ]
PRINTSi PR00348. UBIQUITIN.
SMARTi SM00213. UBQ. 1 hit.
[Graphical view ]
SUPFAMi SSF54236. SSF54236. 1 hit.
SSF57829. SSF57829. 1 hit.
PROSITEi PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The yeast ubiquitin genes: a family of natural gene fusions."
    Oezkaynak E., Finley D., Solomon M.J., Varshavsky A.
    EMBO J. 6:1429-1439(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "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 77-95.
  5. "The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis."
    Finley D., Bartel B., Varshavsky A.
    Nature 338:394-401(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF PROTEIN (S31).
  6. "A proteolytic pathway that recognizes ubiquitin as a degradation signal."
    Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.
    J. Biol. Chem. 270:17442-17456(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
  7. "A ubiquitin mutant with specific defects in DNA repair and multiubiquitination."
    Spence J., Sadis S., Haas A.L., Finley D.
    Mol. Cell. Biol. 15:1265-1273(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYSINE RESIDUES IN UBIQUITIN.
  8. "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 (S31).
  9. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63.
    Strain: SUB592.
  10. "A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
    Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
    Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-48 AND LYS-63.
  11. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-122, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "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-122, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRS27A_YEAST
AccessioniPrimary (citable) accession number: P05759
Secondary accession number(s): D6VYH3
, P04838, P14800, P61864, Q6LA96
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: August 10, 2010
Last modified: September 3, 2014
This is version 135 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Ubiquitin is encoded by several different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins L40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein S37. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.

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

External Data

Dasty 3

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