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Protein

40S ribosomal protein S25-A

Gene

RPS25A

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 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
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-30751-MONOMER.
ReactomeiREACT_188965. SRP-dependent cotranslational protein targeting to membrane.
REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_217188. Formation of a pool of free 40S subunits.
REACT_232946. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_248935. Ribosomal scanning and start codon recognition.
REACT_252688. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_257608. Formation of the ternary complex, and subsequently, the 43S complex.
REACT_257951. Peptide chain elongation.

Names & Taxonomyi

Protein namesi
Recommended name:
40S ribosomal protein S25-A
Alternative name(s):
RP45
S31
YS23
Gene namesi
Name:RPS25A
Synonyms:RPS31A
Ordered Locus Names:YGR027C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VII

Organism-specific databases

CYGDiYGR027c.
SGDiS000003259. RPS25A.

Subcellular locationi

Cytoplasm 1 Publication

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 10810740S ribosomal protein S25-APRO_0000043376Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N,N-dimethylproline; by NTM11 Publication

Keywords - PTMi

Methylation

Proteomic databases

MaxQBiQ3E792.
PaxDbiQ3E792.

Expressioni

Gene expression databases

GenevestigatoriQ3E792.

Interactioni

Subunit structurei

Component of the small 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

Binary interactionsi

WithEntry#Exp.IntActNotes
itself1EBI-16106,EBI-16106

Protein-protein interaction databases

BioGridi33268. 82 interactions.
IntActiQ3E792. 8 interactions.
MINTiMINT-490524.

Structurei

Secondary structure

1
108
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi39 – 413Combined sources
Helixi45 – 539Combined sources
Helixi54 – 563Combined sources
Beta strandi58 – 603Combined sources
Helixi62 – 676Combined sources
Helixi73 – 8311Combined sources
Beta strandi84 – 918Combined sources
Beta strandi95 – 973Combined sources
Beta strandi101 – 1033Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10a1-108[»]
3J6Yelectron microscopy6.10a1-108[»]
3J77electron microscopy6.20Z1-108[»]
3J78electron microscopy6.30Z1-108[»]
3V88X-ray3.00Z1-108[»]
4U3MX-ray3.003/a2-108[»]
4U3NX-ray3.203/a2-108[»]
4U3UX-ray2.903/a2-108[»]
4U4NX-ray3.103/a2-108[»]
4U4OX-ray3.603/a2-108[»]
4U4QX-ray3.003/a2-108[»]
4U4RX-ray2.803/a2-108[»]
4U4UX-ray3.003/a2-108[»]
4U4YX-ray3.203/a2-108[»]
4U4ZX-ray3.103/a2-108[»]
4U50X-ray3.203/a2-108[»]
4U51X-ray3.203/a2-108[»]
4U52X-ray3.003/a2-108[»]
4U53X-ray3.303/a2-108[»]
4U55X-ray3.203/a2-108[»]
4U56X-ray3.453/a2-108[»]
4U6FX-ray3.103/a2-108[»]
4V6Ielectron microscopy-V1-108[»]
4V7RX-ray4.00Q1-108[»]
4V88X-ray3.00Z1-108[»]
4V8Yelectron microscopy4.30Z1-108[»]
4V8Zelectron microscopy6.60Z1-108[»]
4V92electron microscopy3.70Z42-105[»]
ProteinModelPortaliQ3E792.
SMRiQ3E792. Positions 36-105.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein S25e family.Curated

Phylogenomic databases

eggNOGiCOG4901.
GeneTreeiENSGT00390000004856.
HOGENOMiHOG000203673.
InParanoidiQ3E792.
KOiK02975.
OMAiQLIYTRS.
OrthoDBiEOG7647G6.

Family and domain databases

InterProiIPR004977. Ribosomal_S25.
[Graphical view]
PANTHERiPTHR12850. PTHR12850. 1 hit.
PfamiPF03297. Ribosomal_S25. 1 hit.
[Graphical view]
ProDomiPD012268. Ribosomal_S25. 1 hit.
[Graphical view] [Entries sharing at least one domain]

Sequencei

Sequence statusi: Complete.

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

Q3E792-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPPKQQLSKA AKAAAALAGG KKSKKKWSKK SMKDRAQHAV ILDQEKYDRI
60 70 80 90 100
LKEVPTYRYV SVSVLVDRLK IGGSLARIAL RHLEKEGIIK PISKHSKQAI

YTRATASE
Length:108
Mass (Da):12,039
Last modified:November 8, 2005 - v1
Checksum:iC52D0328DEA125B5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti16 – 161A → R AA sequence (PubMed:18782943)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti8 – 81S → F in strain: SK1. 1 Publication
Natural varianti13 – 131A → T in strain: SK1. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03013 Genomic DNA. Translation: CAA26797.1.
Z72812 Genomic DNA. Translation: CAA97010.1.
DQ115389 Genomic DNA. Translation: AAZ22490.1.
EF123137 mRNA. Translation: ABM97481.1.
BK006941 Genomic DNA. Translation: DAA08121.1.
PIRiS05844. R3BY31.
RefSeqiNP_011541.1. NM_001181156.1.

Genome annotation databases

EnsemblFungiiYGR027C; YGR027C; YGR027C.
GeneIDi852911.
KEGGisce:YGR027C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03013 Genomic DNA. Translation: CAA26797.1.
Z72812 Genomic DNA. Translation: CAA97010.1.
DQ115389 Genomic DNA. Translation: AAZ22490.1.
EF123137 mRNA. Translation: ABM97481.1.
BK006941 Genomic DNA. Translation: DAA08121.1.
PIRiS05844. R3BY31.
RefSeqiNP_011541.1. NM_001181156.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10a1-108[»]
3J6Yelectron microscopy6.10a1-108[»]
3J77electron microscopy6.20Z1-108[»]
3J78electron microscopy6.30Z1-108[»]
3V88X-ray3.00Z1-108[»]
4U3MX-ray3.003/a2-108[»]
4U3NX-ray3.203/a2-108[»]
4U3UX-ray2.903/a2-108[»]
4U4NX-ray3.103/a2-108[»]
4U4OX-ray3.603/a2-108[»]
4U4QX-ray3.003/a2-108[»]
4U4RX-ray2.803/a2-108[»]
4U4UX-ray3.003/a2-108[»]
4U4YX-ray3.203/a2-108[»]
4U4ZX-ray3.103/a2-108[»]
4U50X-ray3.203/a2-108[»]
4U51X-ray3.203/a2-108[»]
4U52X-ray3.003/a2-108[»]
4U53X-ray3.303/a2-108[»]
4U55X-ray3.203/a2-108[»]
4U56X-ray3.453/a2-108[»]
4U6FX-ray3.103/a2-108[»]
4V6Ielectron microscopy-V1-108[»]
4V7RX-ray4.00Q1-108[»]
4V88X-ray3.00Z1-108[»]
4V8Yelectron microscopy4.30Z1-108[»]
4V8Zelectron microscopy6.60Z1-108[»]
4V92electron microscopy3.70Z42-105[»]
ProteinModelPortaliQ3E792.
SMRiQ3E792. Positions 36-105.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33268. 82 interactions.
IntActiQ3E792. 8 interactions.
MINTiMINT-490524.

Proteomic databases

MaxQBiQ3E792.
PaxDbiQ3E792.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGR027C; YGR027C; YGR027C.
GeneIDi852911.
KEGGisce:YGR027C.

Organism-specific databases

CYGDiYGR027c.
SGDiS000003259. RPS25A.

Phylogenomic databases

eggNOGiCOG4901.
GeneTreeiENSGT00390000004856.
HOGENOMiHOG000203673.
InParanoidiQ3E792.
KOiK02975.
OMAiQLIYTRS.
OrthoDBiEOG7647G6.

Enzyme and pathway databases

BioCyciYEAST:G3O-30751-MONOMER.
ReactomeiREACT_188965. SRP-dependent cotranslational protein targeting to membrane.
REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_217188. Formation of a pool of free 40S subunits.
REACT_232946. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_248935. Ribosomal scanning and start codon recognition.
REACT_252688. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_257608. Formation of the ternary complex, and subsequently, the 43S complex.
REACT_257951. Peptide chain elongation.

Miscellaneous databases

NextBioi972603.

Gene expression databases

GenevestigatoriQ3E792.

Family and domain databases

InterProiIPR004977. Ribosomal_S25.
[Graphical view]
PANTHERiPTHR12850. PTHR12850. 1 hit.
PfamiPF03297. Ribosomal_S25. 1 hit.
[Graphical view]
ProDomiPD012268. Ribosomal_S25. 1 hit.
[Graphical view] [Entries sharing at least one domain]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The gene for yeast ribosomal protein S31 contains an intron in the leader sequence."
    Nieuwint R.T.M., Molenaar C.M.T., van Bommel J.H., van Raamsdonk-Duin M.M.C., Mager W.H., Planta R.J.
    Curr. Genet. 10:1-5(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Carlsbergensis.
  2. "Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII."
    Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.
    Yeast 13:1077-1090(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(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. "High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing."
    Juneau K., Palm C., Miranda M., Davis R.W.
    Proc. Natl. Acad. Sci. U.S.A. 104:1522-1527(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-96.
    Strain: ATCC 201390 / BY4743.
  6. "Quantitative trait loci mapped to single-nucleotide resolution in yeast."
    Deutschbauer A.M., Davis R.W.
    Nat. Genet. 37:1333-1340(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 5-108, VARIANTS PHE-8 AND THR-13.
    Strain: SK1.
  7. "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 15-22.
  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.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Identification of protein N-terminal methyltransferases in yeast and humans."
    Webb K.J., Lipson R.S., Al-Hadid Q., Whitelegge J.P., Clarke S.G.
    Biochemistry 49:5225-5235(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION AT PRO-2 BY NTM1/TAE1.
  12. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (8.80 ANGSTROMS).
  13. "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 (4.00 ANGSTROMS).
  14. Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS).

Entry informationi

Entry nameiRS25A_YEAST
AccessioniPrimary (citable) accession number: Q3E792
Secondary accession number(s): A2TBN4
, D6VUG0, P05758, P07282, Q45U56
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: November 8, 2005
Last modified: February 4, 2015
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

It is presumed that the precursor part of S25 is engaged in assembling of the small subunit, thus being essential in ribosome maturation.
Present with 322000 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for S25 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 VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: 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.