P04456 (RL25_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
60S ribosomal protein L25

Alternative name(s):
RP16L
YL25
YP42'

Gene names

Name:	RPL25
Ordered Locus Names:	YOL127W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	142 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	This protein binds to a specific region on the 26S rRNA.
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.
Sequence similarities	Belongs to the ribosomal protein L23P family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	RNA-binding rRNA-binding
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	cytoplasmic translation Traceable author statement Ref.7. Source: SGD ribosomal large subunit assembly Inferred from mutant phenotype. Source: SGD
Cellular component	cytosolic large ribosomal subunit Traceable author statement Ref.7. Source: SGD
Molecular function	nucleotide binding Inferred from electronic annotation. Source: InterPro rRNA binding Inferred from electronic annotation. Source: UniProtKB-KW structural constituent of ribosome Traceable author statement Ref.7. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Ref.5 Ref.6
	Chain	2 – 142	141	60S ribosomal protein L25		PRO_0000129483
Amino acid modifications
	Modified residue	29	1	Phosphoserine Ref.8 Ref.9 Ref.10
	Modified residue	59	1	Phosphoserine Ref.9
	Cross-link	61		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.13
Experimental info
	Sequence conflict	106 – 112	7	DVLKVNT → NI in CAA25506. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P04456 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: E40ED3A4FB8CA9F5	FASTA	142	15,758
	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

References

	« Hide 'large scale' referencesShow '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: 6091033] [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: 8896265] [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: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[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: 1544921] [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: 10601260] [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: 9559554] [Abstract] Cited for: NOMENCLATURE, SUBUNIT.
[8]	"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: 11875433] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-29, MASS SPECTROMETRY. Strain: 2124.
[9]	"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: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-29 AND SER-59, MASS SPECTROMETRY.
[10]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-29, MASS SPECTROMETRY.
[11]	"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: 11701127] [Abstract] Cited for: 3D-STRUCTURE MODELING OF 60-136, ELECTRON MICROSCOPY.
[12]	"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: 14976550] [Abstract] Cited for: 3D-STRUCTURE MODELING OF 60-142, ELECTRON MICROSCOPY.
[13]	"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: 15542864] [Abstract] Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-61, MASS SPECTROMETRY. Strain: EJY251-11b.
+	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.

PIR

R5BY25. S63443.

RefSeq

NP_014514.1. NM_001183381.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K5Y	model	-	T	60-136	[»]
1S1I	electron microscopy	11.70	T	60-142	[»]
2WW9	electron microscopy	8.60	K	1-142	[»]
2WWA	electron microscopy	8.90	K	1-142	[»]
3IZS	electron microscopy	-	X	1-142	[»]
3O58	X-ray	4.00	W	1-142	[»]
3O5H	X-ray	4.00	W	1-142	[»]

ProteinModelPortal

P04456.

SMR

P04456. Positions 46-139.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-7137N.

IntAct

P04456. 45 interactions.

MINT

MINT-1488162.

STRING

P04456.

Proteomic databases

PeptideAtlas

P04456.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL127W; YOL127W; YOL127W.

GeneID

853993.

KEGG

sce:YOL127W.

NMPDR

fig|4932.3.peg.5600.

Organism-specific databases

SGD

S000005487. RPL25.

Phylogenomic databases

eggNOG

fuNOG10803.

GeneTree

EFGT00050000004081.

HOGENOM

HBG439330.

OMA

HTTESSM.

OrthoDB

EOG4HMNKV.

Gene expression databases

ArrayExpress

P04456.

Genevestigator

P04456.

GermOnline

YOL127W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

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]

Gene3D

G3DSA:3.30.70.330. a_b_plait_nuc_bd. 1 hit.

KO

K02893.

Pfam

PF00276. Ribosomal_L23. 1 hit.
PF03939. Ribosomal_L23eN. 1 hit.
[Graphical view]

SUPFAM

SSF54189. L23_L15e_core. 1 hit.

PROSITE

PS00050. RIBOSOMAL_L23. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

975479.

Entry information

Entry name

RL25_YEAST

Accession

Primary (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:	December 14, 2011
This is version 120 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program