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P04456 (RL25_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 136. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
60S ribosomal protein L25
Alternative name(s):
RP16L
YL25
YP42'
Gene names
Name:RPL25
Ordered Locus Names:YOL127W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length142 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

This protein binds to a specific region on the 26S rRNA. HAMAP-Rule MF_01369_A

Subunit structure

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). Ref.7

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_01369_A.

Sequence similarities

Belongs to the ribosomal protein L23P family.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.5 Ref.6
Chain2 – 14214160S ribosomal protein L25 HAMAP-Rule MF_01369_A
PRO_0000129483

Amino acid modifications

Cross-link61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.14

Experimental info

Sequence conflict106 – 1127DVLKVNT → NI in CAA25506. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P04456 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: E40ED3A4FB8CA9F5

FASTA14215,758
        10         20         30         40         50         60 
MAPSAKATAA KKAVVKGTNG KKALKVRTSA TFRLPKTLKL ARAPKYASKA VPHYNRLDSY 

        70         80         90        100        110        120 
KVIEQPITSE TAMKKVEDGN ILVFQVSMKA NKYQIKKAVK ELYEVDVLKV NTLVRPNGTK 

       130        140 
KAYVRLTADY DALDIANRIG YI 

« Hide

References

« Hide 'large scale' references
[1]"Structural comparison of yeast ribosomal protein genes."
Leer R.J., van Raamsdonk-Duin M.M.C., Hagendoorn M.J.M., Mager W.H., Planta R.J.
Nucleic Acids Res. 12:6685-6700(1984) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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]"The structure of the eukaryotic ribosome at 3.0 A resolution."
Ben-Shem A., Garreau de Loubresse N., Melnikov S., Jenner L., Yusupova G., Yusupov M.
Science 334:1524-1529(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U41293 Genomic DNA. Translation: AAC49465.1.
X01014 Genomic DNA. Translation: CAA25506.1.
Z74869 Genomic DNA. Translation: CAA99146.1.
BK006948 Genomic DNA. Translation: DAA10657.1.
PIRR5BY25. S63443.
RefSeqNP_014514.1. NM_001183381.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-T60-136[»]
1S1Ielectron microscopy11.70T60-142[»]
2WW9electron microscopy8.60K1-142[»]
2WWAelectron microscopy8.90K1-142[»]
3IZSelectron microscopy-X1-142[»]
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[»]
ProteinModelPortalP04456.
SMRP04456. Positions 23-142.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34248. 153 interactions.
DIPDIP-7137N.
IntActP04456. 54 interactions.
MINTMINT-1488162.
STRING4932.YOL127W.

Proteomic databases

PaxDbP04456.
PeptideAtlasP04456.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOL127W; YOL127W; YOL127W.
GeneID853993.
KEGGsce:YOL127W.

Organism-specific databases

SGDS000005487. RPL25.

Phylogenomic databases

eggNOGCOG0089.
GeneTreeENSGT00390000003263.
HOGENOMHOG000231365.
KOK02893.
OMANRLDSYK.
OrthoDBEOG7Z0K8S.

Enzyme and pathway databases

BioCycYEAST:G3O-33522-MONOMER.

Gene expression databases

GenevestigatorP04456.

Family and domain databases

Gene3D3.30.70.330. 1 hit.
HAMAPMF_01369_A. Ribosomal_L23_A.
InterProIPR012677. 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]
PfamPF00276. Ribosomal_L23. 1 hit.
PF03939. Ribosomal_L23eN. 1 hit.
[Graphical view]
SUPFAMSSF54189. SSF54189. 1 hit.
PROSITEPS00050. RIBOSOMAL_L23. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP04456.
NextBio975479.
PROP04456.

Entry information

Entry nameRL25_YEAST
AccessionPrimary (citable) accession number: P04456
Secondary accession number(s): D6W1U1
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 136 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

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

Yeast

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

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references