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Protein

Ubiquitin-40S ribosomal protein S31

Gene

RPS31

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

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).By similarity
40S ribosomal protein S31: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel.1 Publication

Miscellaneous

Ubiquitin is encoded by several different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins eL40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein eS31. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.Curated

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri121 – 144C4-typeAdd BLAST24

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • protein tag Source: SGD
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) Source: SGD
  • ribosomal small subunit assembly Source: SGD
  • ribosome biogenesis Source: SGD

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32297-MONOMER.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
R-SCE-110320. Translesion Synthesis by POLH.
R-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-SCE-382556. ABC-family proteins mediated transport.
R-SCE-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SCE-5655862. Translesion synthesis by POLK.
R-SCE-5656121. Translesion synthesis by POLI.
R-SCE-5656169. Termination of translesion DNA synthesis.
R-SCE-5675221. Negative regulation of MAPK pathway.
R-SCE-5687128. MAPK6/MAPK4 signaling.
R-SCE-5689603. UCH proteinases.
R-SCE-5689880. Ub-specific processing proteases.
R-SCE-5689901. Metalloprotease DUBs.
R-SCE-5696394. DNA Damage Recognition in GG-NER.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-SCE-5696400. Dual Incision in GG-NER.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-68949. Orc1 removal from chromatin.
R-SCE-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-SCE-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-SCE-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-SCE-72702. Ribosomal scanning and start codon recognition.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
R-SCE-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-SCE-8866654. E3 ubiquitin ligases ubiquitinate target proteins.
R-SCE-917937. Iron uptake and transport.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-40S ribosomal protein S31
Cleaved into the following 2 chains:
40S ribosomal protein S311 Publication
Alternative name(s):
CEP76
S37
Small ribosomal subunit protein eS311 Publication
YS24
Gene namesi
Name:RPS311 Publication
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
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR167W.
SGDiS000004157. RPS31.

Subcellular locationi

Ubiquitin :
40S ribosomal protein S31 :

GO - Cellular componenti

  • cytosolic small ribosomal subunit Source: SGD
  • nucleus Source: UniProtKB-SubCell

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi29K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi48K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi63K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003964871 – 76UbiquitinAdd BLAST76
ChainiPRO_000013768877 – 15240S ribosomal protein S31Add BLAST76

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei122PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP05759.
PRIDEiP05759.

2D gel databases

SWISS-2DPAGEiP61864.

PTM databases

iPTMnetiP05759.

Interactioni

Subunit structurei

Component of the small ribosomal subunit (SSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes) (PubMed:9559554, PubMed:22096102).1 Publication1 Publication

Protein-protein interaction databases

BioGridi31440. 47 interactors.
DIPiDIP-6389N.
IntActiP05759. 19 interactors.
MINTiMINT-8285344.
STRINGi4932.YLR167W.

Structurei

Secondary structure

1152
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi79 – 81Combined sources3
Beta strandi106 – 108Combined sources3
Beta strandi110 – 112Combined sources3
Beta strandi114 – 116Combined sources3
Beta strandi120 – 123Combined sources4
Turni124 – 126Combined sources3
Beta strandi128 – 134Combined sources7
Beta strandi139 – 146Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10311-152[»]
3J6Yelectron microscopy6.10311-152[»]
3J77electron microscopy6.20311-152[»]
3J78electron microscopy6.30311-152[»]
3V88X-ray3.00f1-152[»]
4U3MX-ray3.00E177-152[»]
e178-152[»]
4U3NX-ray3.20E177-152[»]
e178-152[»]
4U3UX-ray2.90E177-152[»]
e178-152[»]
4U4NX-ray3.10E1/e177-152[»]
4U4OX-ray3.60E178-152[»]
e177-152[»]
4U4QX-ray3.00E1/e177-152[»]
4U4RX-ray2.80E1/e177-152[»]
4U4UX-ray3.00E1/e177-152[»]
4U4YX-ray3.20E1/e177-152[»]
4U4ZX-ray3.10E1/e177-152[»]
4U50X-ray3.20E1/e178-152[»]
4U51X-ray3.20E1/e177-152[»]
4U52X-ray3.00E1/e177-152[»]
4U53X-ray3.30E1/e177-152[»]
4U55X-ray3.20E1/e177-152[»]
4U56X-ray3.45E1/e177-152[»]
4U6FX-ray3.10E1/e177-152[»]
4V88X-ray3.00Af/Cf1-152[»]
4V8Yelectron microscopy4.30A51-152[»]
4V8Zelectron microscopy6.60A51-152[»]
4V92electron microscopy3.70f101-152[»]
5DATX-ray3.15E1/e177-152[»]
5DC3X-ray3.25E1/e178-152[»]
5DGEX-ray3.45E1/e177-152[»]
5DGFX-ray3.30E1/e177-152[»]
5DGVX-ray3.10E1/e177-152[»]
5FCIX-ray3.40E1/e177-152[»]
5FCJX-ray3.10E1/e177-152[»]
5I4LX-ray3.10E1/e177-152[»]
5JUOelectron microscopy4.00CC1-152[»]
5JUPelectron microscopy3.50CC1-152[»]
5JUSelectron microscopy4.20CC1-152[»]
5JUTelectron microscopy4.00CC1-152[»]
5JUUelectron microscopy4.00CC1-152[»]
5LYBX-ray3.25E1/e177-152[»]
5M1Jelectron microscopy3.30f282-152[»]
5MC6electron microscopy3.80N1-152[»]
5TGAX-ray3.30E1/e177-152[»]
5TGMX-ray3.50E1/e177-152[»]
5WYJelectron microscopy8.70Sg1-152[»]
ProteinModelPortaliP05759.
SMRiP05759.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 76Ubiquitin-likePROSITE-ProRule annotationAdd BLAST76

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi77 – 99Lys-rich (highly basic)Add BLAST23

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.Curated
In the C-terminal section; belongs to the eukaryotic ribosomal protein eS31 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri121 – 144C4-typeAdd BLAST24

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00880000137943.
HOGENOMiHOG000224977.
InParanoidiP05759.
KOiK02977.
OMAiMSILKYY.
OrthoDBiEOG092C5P9Y.

Family and domain databases

InterProiView protein in InterPro
IPR002906. Ribosomal_S27a.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
PfamiView protein in Pfam
PF01599. Ribosomal_S27. 1 hit.
PF00240. ubiquitin. 1 hit.
PRINTSiPR00348. UBIQUITIN.
SMARTiView protein in SMART
SM01402. Ribosomal_S27. 1 hit.
SM00213. UBQ. 1 hit.
SUPFAMiSSF54236. SSF54236. 1 hit.
SSF57829. SSF57829. 1 hit.
PROSITEiView protein in PROSITE
PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P05759-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGGKKR KKKVYTTPKK IKHKHKKVKL
110 120 130 140 150
AVLSYYKVDA EGKVTKLRRE CSNPTCGAGV FLANHKDRLY CGKCHSVYKV

NA
Length:152
Mass (Da):17,216
Last modified:August 10, 2010 - v3
Checksum:i53BF38E2E2F8B38E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

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 one 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.

Entry informationi

Entry nameiRS31_YEAST
AccessioniPrimary (citable) accession number: P05759
Secondary accession number(s): D6VYH3
, P04838, P14800, P61864, Q6LA96
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: August 10, 2010
Last modified: July 5, 2017
This is version 165 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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