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Protein

50S ribosomal protein L25

Gene

rplY

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding, tRNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L25
Alternative name(s):
General stress protein CTC
Gene namesi
Name:rplY
Synonyms:ctc
Ordered Locus Names:DR_0427
OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Taxonomic identifieri243230 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
Proteomesi
  • UP000002524 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001815431 – 23750S ribosomal protein L25Add BLAST237

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit. Contacts proteins L11 and L16, the A site tRNA, and the 5S and 23S rRNAs.6 Publications

Protein-protein interaction databases

STRINGi243230.DR_0427.

Structurei

Secondary structure

1237
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni11 – 13Combined sources3
Turni15 – 17Combined sources3
Beta strandi18 – 24Combined sources7
Beta strandi26 – 35Combined sources10
Helixi36 – 46Combined sources11
Helixi47 – 49Combined sources3
Beta strandi52 – 55Combined sources4
Beta strandi57 – 59Combined sources3
Beta strandi61 – 72Combined sources12
Turni73 – 76Combined sources4
Beta strandi77 – 85Combined sources9
Beta strandi88 – 90Combined sources3
Beta strandi94 – 97Combined sources4
Beta strandi99 – 102Combined sources4
Turni107 – 110Combined sources4
Beta strandi112 – 114Combined sources3
Beta strandi116 – 123Combined sources8
Beta strandi135 – 137Combined sources3
Beta strandi147 – 149Combined sources3
Beta strandi155 – 157Combined sources3
Beta strandi159 – 162Combined sources4
Beta strandi166 – 172Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NJMX-ray3.60T1-237[»]
1NJPX-ray3.50T1-237[»]
1NKWX-ray3.10T1-237[»]
1NWXX-ray3.50T1-237[»]
1NWYX-ray3.30T1-237[»]
1SM1X-ray3.42T1-237[»]
1XBPX-ray3.50T1-237[»]
2ZJPX-ray3.70S1-237[»]
2ZJQX-ray3.30S1-237[»]
2ZJRX-ray2.91S1-237[»]
3CF5X-ray3.30S1-237[»]
3DLLX-ray3.50S1-237[»]
3PIOX-ray3.25S1-237[»]
3PIPX-ray3.45S1-237[»]
4IO9X-ray3.20S1-237[»]
4IOAX-ray3.20S1-237[»]
4IOCX-ray3.60S1-237[»]
4U67X-ray3.65S1-237[»]
4V49X-ray8.70T1-173[»]
4V4AX-ray9.50T1-173[»]
4V4GX-ray11.50W1-173[»]
4V4PX-ray5.50V1-237[»]
4V4RX-ray5.90Z1-237[»]
4V4SX-ray6.76Z1-237[»]
4V4TX-ray6.46Z1-237[»]
4WFNX-ray3.54S1-237[»]
5DM6X-ray2.90S1-175[»]
5DM7X-ray3.00S1-175[»]
ProteinModelPortaliQ9RX88.
SMRiQ9RX88.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RX88.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 104N-terminal domainAdd BLAST104
Regioni105 – 189Middle domainAdd BLAST85
Regioni190 – 237C-terminal domainAdd BLAST48

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107UH2. Bacteria.
COG1825. LUCA.
HOGENOMiHOG000214906.
InParanoidiQ9RX88.
KOiK02897.
OMAiHTTGKSQ.
OrthoDBiPOG091H03T9.

Family and domain databases

CDDicd00495. Ribosomal_L25_TL5_CTC. 1 hit.
Gene3Di2.170.120.20. 1 hit.
2.40.240.10. 1 hit.
HAMAPiMF_01334. Ribosomal_L25_CTC. 1 hit.
InterProiIPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR029751. Ribosomal_L25.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020057. Ribosomal_L25_b-dom.
IPR001021. Ribosomal_L25_long.
[Graphical view]
PfamiPF01386. Ribosomal_L25p. 1 hit.
PF14693. Ribosomal_TL5_C. 1 hit.
[Graphical view]
ProDomiPD012503. Ribosomal_L25. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF50715. SSF50715. 1 hit.
TIGRFAMsiTIGR00731. bL25_bact_ctc. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9RX88-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELTAKPRTP KQKLDESMIA AVAYNKENNV SFALDRKAFD RAFRQQSTTG
60 70 80 90 100
LFDITVEGGE TFPALVKAVQ MDKRKRAPIH VDFYMVTYGE PVEVSVPVHT
110 120 130 140 150
TGRSQGEVQG GLVDIVVHNL QIVAPGPRRI PQELVVDVTK MNIGDHITAG
160 170 180 190 200
DIKLPEGCTL AADPELTVVS VLPPRLTAEE LEAEVQAAQV AGLVAAGELS
210 220 230
EEAAEAVLEG DASLEEVKAE ASEDNAGTDS EDNSDAQ
Length:237
Mass (Da):25,390
Last modified:March 15, 2004 - v2
Checksum:i1B67F7DD4D385C21
GO

Sequence cautioni

The sequence AAF10004 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF10004.1. Different initiation.
PIRiA75521.
RefSeqiNP_294150.1. NC_001263.1.
WP_010887072.1. NC_001263.1.
WP_027479566.1. NZ_CP015081.1.

Genome annotation databases

EnsemblBacteriaiAAF10004; AAF10004; DR_0427.
GeneIDi1798774.
KEGGidra:DR_0427.
PATRICi21628370. VBIDeiRad64572_0601.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF10004.1. Different initiation.
PIRiA75521.
RefSeqiNP_294150.1. NC_001263.1.
WP_010887072.1. NC_001263.1.
WP_027479566.1. NZ_CP015081.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NJMX-ray3.60T1-237[»]
1NJPX-ray3.50T1-237[»]
1NKWX-ray3.10T1-237[»]
1NWXX-ray3.50T1-237[»]
1NWYX-ray3.30T1-237[»]
1SM1X-ray3.42T1-237[»]
1XBPX-ray3.50T1-237[»]
2ZJPX-ray3.70S1-237[»]
2ZJQX-ray3.30S1-237[»]
2ZJRX-ray2.91S1-237[»]
3CF5X-ray3.30S1-237[»]
3DLLX-ray3.50S1-237[»]
3PIOX-ray3.25S1-237[»]
3PIPX-ray3.45S1-237[»]
4IO9X-ray3.20S1-237[»]
4IOAX-ray3.20S1-237[»]
4IOCX-ray3.60S1-237[»]
4U67X-ray3.65S1-237[»]
4V49X-ray8.70T1-173[»]
4V4AX-ray9.50T1-173[»]
4V4GX-ray11.50W1-173[»]
4V4PX-ray5.50V1-237[»]
4V4RX-ray5.90Z1-237[»]
4V4SX-ray6.76Z1-237[»]
4V4TX-ray6.46Z1-237[»]
4WFNX-ray3.54S1-237[»]
5DM6X-ray2.90S1-175[»]
5DM7X-ray3.00S1-175[»]
ProteinModelPortaliQ9RX88.
SMRiQ9RX88.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0427.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF10004; AAF10004; DR_0427.
GeneIDi1798774.
KEGGidra:DR_0427.
PATRICi21628370. VBIDeiRad64572_0601.

Phylogenomic databases

eggNOGiENOG4107UH2. Bacteria.
COG1825. LUCA.
HOGENOMiHOG000214906.
InParanoidiQ9RX88.
KOiK02897.
OMAiHTTGKSQ.
OrthoDBiPOG091H03T9.

Miscellaneous databases

EvolutionaryTraceiQ9RX88.

Family and domain databases

CDDicd00495. Ribosomal_L25_TL5_CTC. 1 hit.
Gene3Di2.170.120.20. 1 hit.
2.40.240.10. 1 hit.
HAMAPiMF_01334. Ribosomal_L25_CTC. 1 hit.
InterProiIPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR029751. Ribosomal_L25.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020057. Ribosomal_L25_b-dom.
IPR001021. Ribosomal_L25_long.
[Graphical view]
PfamiPF01386. Ribosomal_L25p. 1 hit.
PF14693. Ribosomal_TL5_C. 1 hit.
[Graphical view]
ProDomiPD012503. Ribosomal_L25. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF50715. SSF50715. 1 hit.
TIGRFAMsiTIGR00731. bL25_bact_ctc. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRL25_DEIRA
AccessioniPrimary (citable) accession number: Q9RX88
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: March 15, 2004
Last modified: November 2, 2016
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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

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.