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P04456

- RL25_YEAST

UniProt

P04456 - RL25_YEAST

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Protein

60S ribosomal protein L25

Gene
RPL25, YOL127W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

This protein binds to a specific region on the 26S rRNA.UniRule annotation

GO - Molecular functioni

  1. nucleotide binding Source: InterPro
  2. protein binding Source: IntAct
  3. RNA binding Source: SGD
  4. rRNA binding Source: UniProtKB-KW
  5. structural constituent of ribosome Source: SGD

GO - Biological processi

  1. cytoplasmic translation Source: SGD
  2. ribosomal large subunit assembly Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33522-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.

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L25
Alternative name(s):
RP16L
YL25
YP42'
Gene namesi
Name:RPL25
Ordered Locus Names:YOL127W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

SGDiS000005487. RPL25.

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed2 Publications
Chaini2 – 14214160S ribosomal protein L25UniRule annotationPRO_0000129483Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki61 – 61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP04456.
PaxDbiP04456.
PeptideAtlasiP04456.

Expressioni

Gene expression databases

GenevestigatoriP04456.

Interactioni

Subunit structurei

Component of the large 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
BTT1P403143EBI-15308,EBI-3802
EGD1Q026424EBI-15308,EBI-6371
NPL3Q015602EBI-15308,EBI-12114

Protein-protein interaction databases

BioGridi34248. 153 interactions.
DIPiDIP-7137N.
IntActiP04456. 54 interactions.
MINTiMINT-1488162.
STRINGi4932.YOL127W.

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-T60-136[»]
1S1Ielectron microscopy11.70T60-142[»]
1VW8electron microscopy6.10Y1-142[»]
1VWUelectron microscopy6.10Y1-142[»]
2WW9electron microscopy8.60K1-142[»]
2WWAelectron microscopy8.90K1-142[»]
2WWBelectron microscopy6.48K1-142[»]
3IZSelectron microscopy-X1-142[»]
3J65electron microscopy8.70W1-142[»]
3O58X-ray4.00W1-142[»]
3O5HX-ray4.00W1-142[»]
3U5EX-ray3.00X1-142[»]
3U5IX-ray3.00X1-142[»]
4B6Aelectron microscopy8.10X1-142[»]
4BYNelectron microscopy4.30X2-142[»]
4BYUelectron microscopy6.60X2-142[»]
4CUWelectron microscopy3.70X1-142[»]
ProteinModelPortaliP04456.
SMRiP04456. Positions 23-142.

Miscellaneous databases

EvolutionaryTraceiP04456.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0089.
GeneTreeiENSGT00390000003263.
HOGENOMiHOG000231365.
KOiK02893.
OMAiKAVPHYN.
OrthoDBiEOG7Z0K8S.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
HAMAPiMF_01369_A. Ribosomal_L23_A.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR012678. Ribosomal_L23/L15e_core_dom.
IPR001014. Ribosomal_L23/L25_CS.
IPR005633. Ribosomal_L23/L25_N.
IPR013025. Ribosomal_L25/23.
[Graphical view]
PfamiPF00276. Ribosomal_L23. 1 hit.
PF03939. Ribosomal_L23eN. 1 hit.
[Graphical view]
SUPFAMiSSF54189. SSF54189. 1 hit.
PROSITEiPS00050. RIBOSOMAL_L23. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P04456-1 [UniParc]FASTAAdd to Basket

« Hide

MAPSAKATAA KKAVVKGTNG KKALKVRTSA TFRLPKTLKL ARAPKYASKA    50
VPHYNRLDSY KVIEQPITSE TAMKKVEDGN ILVFQVSMKA NKYQIKKAVK 100
ELYEVDVLKV NTLVRPNGTK KAYVRLTADY DALDIANRIG YI 142
Length:142
Mass (Da):15,758
Last modified:January 23, 2007 - v4
Checksum:iE40ED3A4FB8CA9F5
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti106 – 1127DVLKVNT → NI in CAA25506. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U41293 Genomic DNA. Translation: AAC49465.1.
X01014 Genomic DNA. Translation: CAA25506.1.
Z74869 Genomic DNA. Translation: CAA99146.1.
BK006948 Genomic DNA. Translation: DAA10657.1.
PIRiS63443. R5BY25.
RefSeqiNP_014514.1. NM_001183381.1.

Genome annotation databases

EnsemblFungiiYOL127W; YOL127W; YOL127W.
GeneIDi853993.
KEGGisce:YOL127W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U41293 Genomic DNA. Translation: AAC49465.1 .
X01014 Genomic DNA. Translation: CAA25506.1 .
Z74869 Genomic DNA. Translation: CAA99146.1 .
BK006948 Genomic DNA. Translation: DAA10657.1 .
PIRi S63443. R5BY25.
RefSeqi NP_014514.1. NM_001183381.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1K5Y model - T 60-136 [» ]
1S1I electron microscopy 11.70 T 60-142 [» ]
1VW8 electron microscopy 6.10 Y 1-142 [» ]
1VWU electron microscopy 6.10 Y 1-142 [» ]
2WW9 electron microscopy 8.60 K 1-142 [» ]
2WWA electron microscopy 8.90 K 1-142 [» ]
2WWB electron microscopy 6.48 K 1-142 [» ]
3IZS electron microscopy - X 1-142 [» ]
3J65 electron microscopy 8.70 W 1-142 [» ]
3O58 X-ray 4.00 W 1-142 [» ]
3O5H X-ray 4.00 W 1-142 [» ]
3U5E X-ray 3.00 X 1-142 [» ]
3U5I X-ray 3.00 X 1-142 [» ]
4B6A electron microscopy 8.10 X 1-142 [» ]
4BYN electron microscopy 4.30 X 2-142 [» ]
4BYU electron microscopy 6.60 X 2-142 [» ]
4CUW electron microscopy 3.70 X 1-142 [» ]
ProteinModelPortali P04456.
SMRi P04456. Positions 23-142.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34248. 153 interactions.
DIPi DIP-7137N.
IntActi P04456. 54 interactions.
MINTi MINT-1488162.
STRINGi 4932.YOL127W.

Proteomic databases

MaxQBi P04456.
PaxDbi P04456.
PeptideAtlasi P04456.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOL127W ; YOL127W ; YOL127W .
GeneIDi 853993.
KEGGi sce:YOL127W.

Organism-specific databases

SGDi S000005487. RPL25.

Phylogenomic databases

eggNOGi COG0089.
GeneTreei ENSGT00390000003263.
HOGENOMi HOG000231365.
KOi K02893.
OMAi KAVPHYN.
OrthoDBi EOG7Z0K8S.

Enzyme and pathway databases

BioCyci YEAST:G3O-33522-MONOMER.
Reactomei REACT_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.

Miscellaneous databases

EvolutionaryTracei P04456.
NextBioi 975479.
PROi P04456.

Gene expression databases

Genevestigatori P04456.

Family and domain databases

Gene3Di 3.30.70.330. 1 hit.
HAMAPi MF_01369_A. Ribosomal_L23_A.
InterProi IPR012677. Nucleotide-bd_a/b_plait.
IPR012678. Ribosomal_L23/L15e_core_dom.
IPR001014. Ribosomal_L23/L25_CS.
IPR005633. Ribosomal_L23/L25_N.
IPR013025. Ribosomal_L25/23.
[Graphical view ]
Pfami PF00276. Ribosomal_L23. 1 hit.
PF03939. Ribosomal_L23eN. 1 hit.
[Graphical view ]
SUPFAMi SSF54189. SSF54189. 1 hit.
PROSITEi PS00050. RIBOSOMAL_L23. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Carlsbergensis.
  2. "Sequence analysis of a 13.4 kbp fragment from the left arm of chromosome XV reveals a malate dehydrogenase gene, a putative Ser/Thr protein kinase, the ribosomal L25 gene and four new open reading frames."
    Casamayor A., Khalid H., Balcells L., Aldea M., Casas C., Herrero E., Arino J.
    Yeast 12:1013-1020(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(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. "NH2-terminal acetylation of ribosomal proteins of Saccharomyces cerevisiae."
    Takakura H., Tsunasawa S., Miyagi M., Warner J.R.
    J. Biol. Chem. 267:5442-5445(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-21.
  6. "The action of N-terminal acetyltransferases on yeast ribosomal proteins."
    Arnold R.J., Polevoda B., Reilly J.P., Sherman F.
    J. Biol. Chem. 274:37035-37040(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE OF INITIATOR METHIONINE.
  7. "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.
  8. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "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].
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
    Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
    Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions."
    Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J.
    Cell 107:373-386(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 60-136, ELECTRON MICROSCOPY.
  13. "Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation."
    Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J.
    EMBO J. 23:1008-1019(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 60-142, ELECTRON MICROSCOPY.
  14. "A proteomic strategy for gaining insights into protein sumoylation in yeast."
    Denison C., Rudner A.D., Gerber S.A., Bakalarski C.E., Moazed D., Gygi S.P.
    Mol. Cell. Proteomics 4:246-254(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-61.
    Strain: EJY251-11b.
  15. "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 (4.0 ANGSTROMS) OF 80S RIBOSOME.
  16. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.

Entry informationi

Entry nameiRL25_YEAST
AccessioniPrimary (citable) accession number: P04456
Secondary accession number(s): D6W1U1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: September 3, 2014
This is version 139 of the entry and version 4 of the sequence. [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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

External Data

Dasty 3

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