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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: -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-110314 Recognition of DNA damage by PCNA-containing replication complex
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-187577 SCF(Skp2)-mediated degradation of p27/p21
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-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
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-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-9033241 Peroxisomal protein import
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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei122PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein

Proteomic databases

MaxQBiP05759
PaxDbiP05759
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, 52 interactors
DIPiDIP-6389N
IntActiP05759, 19 interactors
MINTiP05759
STRINGi4932.YLR167W

Structurei

Secondary structure

1152
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi12 – 16Combined sources5
Helixi23 – 34Combined sources12
Helixi38 – 40Combined sources3
Beta strandi42 – 45Combined sources4
Beta strandi47 – 49Combined sources3
Helixi57 – 59Combined sources3
Beta strandi66 – 70Combined sources5

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[»]
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[»]
5L6HX-ray2.30B/D/E1-76[»]
5L6IX-ray2.76B/D/E1-76[»]
5L6JX-ray2.68B/D1-76[»]
5LYBX-ray3.25E1/e177-152[»]
5M1Jelectron microscopy3.30f282-152[»]
5MC6electron microscopy3.80N1-152[»]
5NDGX-ray3.70E1/e11-152[»]
5NDWX-ray3.70E1/e180-152[»]
5OBMX-ray3.40E1/e181-152[»]
5TGAX-ray3.30E1/e177-152[»]
5TGMX-ray3.50E1/e177-152[»]
5U4PX-ray2.50C1-76[»]
5WYJelectron microscopy8.70Sg1-152[»]
6EMLelectron microscopy3.60N1-152[»]
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

GeneTreeiENSGT00910000144152
HOGENOMiHOG000224977
InParanoidiP05759
KOiK02977
OMAiMSILKYY
OrthoDBiEOG092C5P9Y

Family and domain databases

Gene3Di2.20.25.660, 1 hit
InterProiView protein in InterPro
IPR002906 Ribosomal_S27a
IPR011332 Ribosomal_zn-bd
IPR038582 S27a-like_sf
IPR019956 Ubiquitin
IPR029071 Ubiquitin-like_domsf
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

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: May 23, 2018
This is version 174 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

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