Ubiquitin-40S ribosomal protein S31 precursor - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P05759 (RS27A_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 121. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ubiquitin-40S ribosomal protein S31

Cleaved into the following 2 chains:

Ubiquitin
40S ribosomal protein S31
Alternative name(s):
CEP76
S37
YS24

Gene names

Name:	RPS31
Synonyms:	RPS37, UBI3
Ordered Locus Names:	YLR167W
ORF Names:	L9470.14

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	152 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subunit structure	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). Ref.9
Subcellular location	Ubiquitin: Cytoplasm By similarity. Nucleus By similarity. 40S ribosomal protein S31: Cytoplasm By similarity.
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.
Sequence similarities	In the N-terminal section; belongs to the ubiquitin family. In the C-terminal section; belongs to the ribosomal protein S27Ae family. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Cytoplasm Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW cytoplasmic translation Inferred by curator PubMed 18782943 PubMed 385049. Source: SGD maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) Inferred from mutant phenotype Ref.6. Source: SGD ribosomal small subunit assembly Inferred from mutant phenotype PubMed 9830035. Source: SGD
Cellular_component	cytosolic small ribosomal subunit Inferred from direct assay PubMed 18782943 PubMed 385049. Source: SGD nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein tag Inferred from mutant phenotype Ref.6. Source: SGD structural constituent of ribosome Inferred by curator PubMed 18782943 PubMed 385049. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 76

Ubiquitin

PRO_0000396487

Chain

77 – 152

40S ribosomal protein S31

PRO_0000137688

Regions

Domain

1 – 76

Ubiquitin-like

Zinc finger

121 – 144

C4-type

Compositional bias

77 – 99

Lys-rich (highly basic)

Amino acid modifications

Modified residue

Phosphoserine Ref.4 Ref.13

Modified residue

Phosphothreonine Ref.10

Modified residue

122

Phosphoserine Ref.12 Ref.13

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4 Ref.11

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4 Ref.11

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4 Ref.11

Cross-link

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Experimental info

Mutagenesis

K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.7 Ref.8

Mutagenesis

K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.7 Ref.8

Mutagenesis

K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. Ref.7 Ref.8

Secondary structure

152

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P05759 [UniParc].

Last modified August 10, 2010. Version 3.
Checksum: 53BF38E2E2F8B38E
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FASTA

152

17,216

        10         20         30         40         50         60 
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 

        70         80         90        100        110        120 
IQKESTLHLV LRLRGGGKKR KKKVYTTPKK IKHKHKKVKL AVLSYYKVDA EGKVTKLRRE 

       130        140        150 
CSNPTCGAGV FLANHKDRLY CGKCHSVYKV NA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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. Hoheisel J.D. Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 43-53, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-57, UBIQUITINATION AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63, MASS SPECTROMETRY. Strain: SUB592.
[5]	"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) Cited for: PROTEIN SEQUENCE OF 77-95.
[6]	"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).
[7]	"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.
[8]	"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.
[9]	"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).
[10]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-87, MASS SPECTROMETRY (S31). Strain: 2124.
[11]	"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, MASS SPECTROMETRY.
[12]	"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, MASS SPECTROMETRY (S31).
[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-57 AND SER-122, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X05730 Genomic DNA. Translation: CAA29197.1.
U17246 Genomic DNA. Translation: AAB67466.1.
BK006945 Genomic DNA. Translation: DAA09489.1.

PIR

UQBYR7. C29456.

RefSeq

NP_013268.1. NM_001182054.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3U5C	X-ray	3.00	f	1-152	[»]
3U5G	X-ray	3.00	f	1-152	[»]

ProteinModelPortal

P05759.

SMR

P05759. Positions 1-74, 102-149.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6389N.

IntAct

P05759. 14 interactions.

MINT

MINT-8285344.

STRING

4932.YLR167W.

2D gel databases

SWISS-2DPAGE

P61864.

Proteomic databases

PaxDb

P05759.

PRIDE

P05759.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YLR167W; YLR167W; YLR167W.

GeneID

850864.

KEGG

sce:YLR167W.

Organism-specific databases

SGD

S000004157. RPS31.

Phylogenomic databases

eggNOG

COG5272.

GeneTree

ENSGT00550000074763.

HOGENOM

HOG000224977.

K02977.

OMA

KKVYTTP.

OrthoDB

EOG4F21CP.

Enzyme and pathway databases

BioCyc

YEAST:G3O-32297-MONOMER.

Gene expression databases

ArrayExpress

P05759.

Genevestigator

P61864.

GermOnline

YIL148W. Saccharomyces cerevisiae.
YKR094C. Saccharomyces cerevisiae.
YLL039C. Saccharomyces cerevisiae.
YLR167W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR002906. Ribosomal_S27a.
IPR000626. Ubiquitin.
IPR019954. Ubiquitin_CS.
IPR019956. Ubiquitin_subgr.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF01599. Ribosomal_S27. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]

PRINTS

PR00348. UBIQUITIN.

SMART

SM00213. UBQ. 1 hit.
[Graphical view]

PROSITE

PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

967191.

Entry information

Entry name

RS27A_YEAST

Accession

Primary (citable) accession number: P05759
Secondary accession number(s): D6VYH3

Q6LA96

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1988
Last sequence update:	August 10, 2010
Last modified:	May 29, 2013
This is version 121 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XII

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

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Cleaved into the following 2 chains:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents