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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

Enzyme and pathway databases

BioCyciDRAD243230:GH46-438-MONOMER.

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 23723750S ribosomal protein L25PRO_0000181543Add
BLAST

Proteomic databases

PRIDEiQ9RX88.

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

1
237
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni11 – 133Combined sources
Turni15 – 173Combined sources
Beta strandi18 – 247Combined sources
Beta strandi26 – 3510Combined sources
Helixi36 – 4611Combined sources
Helixi47 – 493Combined sources
Beta strandi52 – 554Combined sources
Beta strandi57 – 593Combined sources
Beta strandi61 – 7212Combined sources
Turni73 – 764Combined sources
Beta strandi77 – 859Combined sources
Beta strandi88 – 903Combined sources
Beta strandi94 – 974Combined sources
Beta strandi99 – 1024Combined sources
Turni107 – 1104Combined sources
Beta strandi112 – 1143Combined sources
Beta strandi116 – 1238Combined sources
Beta strandi135 – 1373Combined sources
Beta strandi147 – 1493Combined sources
Beta strandi155 – 1573Combined sources
Beta strandi159 – 1624Combined sources
Beta strandi166 – 1727Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-177.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RX88.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 104104N-terminal domainAdd
BLAST
Regioni105 – 18985Middle domainAdd
BLAST
Regioni190 – 23748C-terminal domainAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107UH2. Bacteria.
COG1825. LUCA.
HOGENOMiHOG000214906.
InParanoidiQ9RX88.
KOiK02897.
OMAiVQMDKRK.
OrthoDBiEOG6SZ1PC.

Family and domain databases

Gene3Di2.170.120.20. 1 hit.
2.40.240.10. 1 hit.
HAMAPiMF_01334. Ribosomal_L25_CTC.
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 AAF10004.1 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.

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-177.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0427.

Proteomic databases

PRIDEiQ9RX88.

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.
OMAiVQMDKRK.
OrthoDBiEOG6SZ1PC.

Enzyme and pathway databases

BioCyciDRAD243230:GH46-438-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9RX88.

Family and domain databases

Gene3Di2.170.120.20. 1 hit.
2.40.240.10. 1 hit.
HAMAPiMF_01334. Ribosomal_L25_CTC.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  2. "Protein recycling is a major component of post-irradiation recovery in Deinococcus radiodurans strain R1."
    Joshi B.S., Schmid R., Altendorf K., Apte S.K.
    Biochem. Biophys. Res. Commun. 320:1112-1117(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-22.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  3. "High resolution structure of the large ribosomal subunit from a mesophilic eubacterium."
    Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., Yonath A.
    Cell 107:679-688(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT, PROTEIN SEQUENCE OF 1-5.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  4. "Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria."
    Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R., Yonath A., Franceschi F.
    Nature 413:814-821(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FIVE ANTIBIOTICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  5. "Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression."
    Bashan A., Agmon I., Zarivach R., Schluenzen F., Harms J., Berisio R., Bartels H., Franceschi F., Auerbach T., Hansen H.A., Kossoy E., Kessler M., Yonath A.
    Mol. Cell 11:91-102(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TRNA MIMICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  6. "Structural basis for the antibiotic activity of ketolides and azalides."
    Schluenzen F., Harms J.M., Franceschi F., Hansen H.A., Bartels H., Zarivach R., Yonath A.
    Structure 11:329-338(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH MODIFIED MACROLIDE ANTIBIOTICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  7. "Structural insight into the role of the ribosomal tunnel in cellular regulation."
    Berisio R., Schluenzen F., Harms J., Bashan A., Auerbach T., Baram D., Yonath A.
    Nat. Struct. Biol. 10:366-370(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TROLEANDOMYCIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  8. "Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin."
    Harms J.M., Schluenzen F., Fucini P., Bartels H., Yonath A.
    BMC Biol. 2:4-4(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH THE STREPTOGRAMINS QUINUPRISTIN AND DALFOPRISTIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  9. "Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin."
    Schluenzen F., Pyetan E., Fucini P., Yonath A., Harms J.M.
    Mol. Microbiol. 54:1287-1294(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TIAMULIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.

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: May 11, 2016
This is version 119 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.