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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

Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel. uL23 is a major component of the universal docking site for these factors at the polypeptide exit tunnel.1 Publication

GO - Molecular functioni

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

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • ribosomal large subunit assembly Source: SGD
  • translation Source: GO_Central

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33522-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L251 Publication
Alternative name(s):
Large ribosomal subunit protein uL231 Publication
RP16L
YL25
YP42'
Gene namesi
Name:RPL251 Publication
Ordered Locus Names:YOL127W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL127W.
SGDiS000005487. RPL25.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD
  • preribosome, large subunit precursor Source: SGD

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00001294832 – 14260S ribosomal protein L25Add BLAST141

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP04456.
PRIDEiP04456.
TopDownProteomicsiP04456.

PTM databases

iPTMnetiP04456.

Interactioni

Subunit structurei

Component of the large ribosomal subunit (LSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes). uL23 is associated with the polypeptide exit tunnel (PubMed:9559554, PubMed:22096102).1 Publication1 Publication

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi34248. 74 interactors.
DIPiDIP-7137N.
IntActiP04456. 55 interactors.
MINTiMINT-1488162.
STRINGi4932.YOL127W.

Structurei

Secondary structure

1142
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi28 – 30Combined sources3
Beta strandi48 – 51Combined sources4
Helixi59 – 62Combined sources4
Beta strandi63 – 66Combined sources4
Helixi70 – 79Combined sources10
Beta strandi81 – 86Combined sources6
Helixi92 – 103Combined sources12
Beta strandi107 – 114Combined sources8
Turni116 – 118Combined sources3
Beta strandi120 – 126Combined sources7
Helixi132 – 139Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
3JCTelectron microscopy3.08X1-142[»]
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[»]
5APNelectron microscopy3.91X1-142[»]
5APOelectron microscopy3.41X1-142[»]
5DATX-ray3.15N5/n52-142[»]
5DC3X-ray3.25N5/n52-142[»]
5DGEX-ray3.45N5/n52-142[»]
5DGFX-ray3.30N5/n52-142[»]
5DGVX-ray3.10N5/n52-142[»]
5FCIX-ray3.40N5/n52-142[»]
5FCJX-ray3.10N5/n52-142[»]
5FL8electron microscopy9.50X1-142[»]
5GAKelectron microscopy3.88Z1-142[»]
5H4Pelectron microscopy3.07X1-142[»]
5I4LX-ray3.10N5/n522-142[»]
5JCSelectron microscopy9.50X1-142[»]
5JUOelectron microscopy4.00CA1-142[»]
5JUPelectron microscopy3.50CA1-142[»]
5JUSelectron microscopy4.20CA1-142[»]
5JUTelectron microscopy4.00CA1-142[»]
5JUUelectron microscopy4.00CA1-142[»]
5LYBX-ray3.25N5/n522-142[»]
5M1Jelectron microscopy3.30X522-142[»]
5MC6electron microscopy3.80AH1-142[»]
5T62electron microscopy3.30k1-142[»]
5T6Relectron microscopy4.50k1-142[»]
5TGAX-ray3.30N5/n522-142[»]
5TGMX-ray3.50N5/n522-142[»]
ProteinModelPortaliP04456.
SMRiP04456.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04456.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000003263.
HOGENOMiHOG000231365.
InParanoidiP04456.
KOiK02893.
OMAiHKVIIHP.
OrthoDBiEOG092C5BSI.

Family and domain databases

HAMAPiMF_01369_A. Ribosomal_L23_A. 1 hit.
InterProiView protein in InterPro
IPR012678. Ribosomal_L23/L15e_core_dom.
IPR001014. Ribosomal_L23/L25_CS.
IPR005633. Ribosomal_L23/L25_N.
IPR013025. Ribosomal_L25/23.
PfamiView protein in Pfam
PF00276. Ribosomal_L23. 1 hit.
PF03939. Ribosomal_L23eN. 1 hit.
SUPFAMiSSF54189. SSF54189. 1 hit.
PROSITEiView protein in PROSITE
PS00050. RIBOSOMAL_L23. 1 hit.

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)DescriptionActionsGraphical viewLength
Sequence conflicti106 – 112DVLKVNT → NI in CAA25506 (PubMed:6091033).Curated7

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.

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 one 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.

Entry informationi

Entry nameiRL25_YEAST
AccessioniPrimary (citable) accession number: P04456
Secondary accession number(s): D6W1U1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: July 5, 2017
This is version 172 of the entry and version 4 of the sequence. See 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