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Protein

60S ribosomal protein L25

Gene

RPL25

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

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

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • RNA binding Source: SGD
  • rRNA binding Source: UniProtKB-KW
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • 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_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.

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 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL127W.
SGDiS000005487. RPL25.

Subcellular locationi

GO - Cellular componenti

  • 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 L25PRO_0000129483Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP04456.
PaxDbiP04456.
PeptideAtlasiP04456.

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

Structurei

Secondary structure

1
142
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi28 – 303Combined sources
Beta strandi48 – 514Combined sources
Helixi59 – 624Combined sources
Beta strandi63 – 664Combined sources
Helixi70 – 7910Combined sources
Beta strandi81 – 866Combined sources
Helixi92 – 10312Combined sources
Beta strandi107 – 1148Combined sources
Turni116 – 1183Combined sources
Beta strandi120 – 1267Combined sources
Helixi132 – 1398Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-T60-136[»]
2WW9electron microscopy8.60K1-142[»]
2WWAelectron microscopy8.90K1-142[»]
2WWBelectron microscopy6.48K1-142[»]
3J6Xelectron microscopy6.10651-142[»]
3J6Yelectron microscopy6.10651-142[»]
3J77electron microscopy6.20751-142[»]
3J78electron microscopy6.30751-142[»]
4U3MX-ray3.00N5/n52-142[»]
4U3NX-ray3.20N5/n52-142[»]
4U3UX-ray2.90N5/n52-142[»]
4U4NX-ray3.10N5/n52-142[»]
4U4OX-ray3.60N5/n52-142[»]
4U4QX-ray3.00N5/n52-142[»]
4U4RX-ray2.80N5/n52-142[»]
4U4UX-ray3.00N5/n52-142[»]
4U4YX-ray3.20N5/n52-142[»]
4U4ZX-ray3.10N5/n52-142[»]
4U50X-ray3.20N5/n52-142[»]
4U51X-ray3.20N5/n52-142[»]
4U52X-ray3.00N5/n52-142[»]
4U53X-ray3.30N5/n52-142[»]
4U55X-ray3.20N5/n52-142[»]
4U56X-ray3.45N5/n52-142[»]
4U6FX-ray3.10N5/n52-142[»]
4V4Belectron microscopy11.70BT60-142[»]
4V6Ielectron microscopy8.80BX1-142[»]
4V7Felectron microscopy8.70W1-142[»]
4V7RX-ray4.00BW/DW1-142[»]
4V88X-ray3.00BX/DX1-142[»]
4V8Telectron microscopy8.10X1-142[»]
4V8Yelectron microscopy4.30BX2-142[»]
4V8Zelectron microscopy6.60BX2-142[»]
4V91electron microscopy3.70X1-142[»]
ProteinModelPortaliP04456.
SMRiP04456. Positions 57-139.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04456.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L23P family.Curated

Phylogenomic databases

eggNOGiCOG0089.
GeneTreeiENSGT00390000003263.
HOGENOMiHOG000231365.
InParanoidiP04456.
KOiK02893.
OMAiFPRKSAP.
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

        10         20         30         40         50
MAPSAKATAA KKAVVKGTNG KKALKVRTSA TFRLPKTLKL ARAPKYASKA
60 70 80 90 100
VPHYNRLDSY KVIEQPITSE TAMKKVEDGN ILVFQVSMKA NKYQIKKAVK
110 120 130 140
ELYEVDVLKV NTLVRPNGTK KAYVRLTADY DALDIANRIG YI
Length:142
Mass (Da):15,758
Last modified:January 23, 2007 - v4
Checksum:iE40ED3A4FB8CA9F5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti106 – 1127DVLKVNT → NI in CAA25506 (PubMed:6091033).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-T60-136[»]
2WW9electron microscopy8.60K1-142[»]
2WWAelectron microscopy8.90K1-142[»]
2WWBelectron microscopy6.48K1-142[»]
3J6Xelectron microscopy6.10651-142[»]
3J6Yelectron microscopy6.10651-142[»]
3J77electron microscopy6.20751-142[»]
3J78electron microscopy6.30751-142[»]
4U3MX-ray3.00N5/n52-142[»]
4U3NX-ray3.20N5/n52-142[»]
4U3UX-ray2.90N5/n52-142[»]
4U4NX-ray3.10N5/n52-142[»]
4U4OX-ray3.60N5/n52-142[»]
4U4QX-ray3.00N5/n52-142[»]
4U4RX-ray2.80N5/n52-142[»]
4U4UX-ray3.00N5/n52-142[»]
4U4YX-ray3.20N5/n52-142[»]
4U4ZX-ray3.10N5/n52-142[»]
4U50X-ray3.20N5/n52-142[»]
4U51X-ray3.20N5/n52-142[»]
4U52X-ray3.00N5/n52-142[»]
4U53X-ray3.30N5/n52-142[»]
4U55X-ray3.20N5/n52-142[»]
4U56X-ray3.45N5/n52-142[»]
4U6FX-ray3.10N5/n52-142[»]
4V4Belectron microscopy11.70BT60-142[»]
4V6Ielectron microscopy8.80BX1-142[»]
4V7Felectron microscopy8.70W1-142[»]
4V7RX-ray4.00BW/DW1-142[»]
4V88X-ray3.00BX/DX1-142[»]
4V8Telectron microscopy8.10X1-142[»]
4V8Yelectron microscopy4.30BX2-142[»]
4V8Zelectron microscopy6.60BX2-142[»]
4V91electron microscopy3.70X1-142[»]
ProteinModelPortaliP04456.
SMRiP04456. Positions 57-139.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34248. 156 interactions.
DIPiDIP-7137N.
IntActiP04456. 54 interactions.
MINTiMINT-1488162.
STRINGi4932.YOL127W.

Proteomic databases

MaxQBiP04456.
PaxDbiP04456.
PeptideAtlasiP04456.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YOL127W.
SGDiS000005487. RPL25.

Phylogenomic databases

eggNOGiCOG0089.
GeneTreeiENSGT00390000003263.
HOGENOMiHOG000231365.
InParanoidiP04456.
KOiK02893.
OMAiFPRKSAP.
OrthoDBiEOG7Z0K8S.

Enzyme and pathway databases

BioCyciYEAST:G3O-33522-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.

Miscellaneous databases

EvolutionaryTraceiP04456.
NextBioi975479.
PROiP04456.

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]
ProtoNetiSearch...

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: June 24, 2015
This is version 149 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

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.