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Protein

50S ribosomal protein L5

Gene

rplE

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 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement (By similarity). Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.By similarity

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:GH46-333-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L5
Gene namesi
Name:rplE
Ordered Locus Names:DR_0323
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 – 18018050S ribosomal protein L5PRO_0000124923Add
BLAST

Proteomic databases

PRIDEiQ9RXJ0.

Interactioni

Subunit structurei

Forms a bridge to the 30S subunit in the 70S ribosome (By similarity). Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 (CTC) subcomplex. Is known to contact the 5S rRNA, 23S rRNA and the P site tRNA.By similarity6 Publications

Protein-protein interaction databases

STRINGi243230.DR_0323.

Structurei

Secondary structure

1
180
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 2017Combined sources
Beta strandi25 – 284Combined sources
Beta strandi33 – 353Combined sources
Beta strandi36 – 383Combined sources
Beta strandi42 – 443Combined sources
Helixi47 – 6115Combined sources
Beta strandi66 – 694Combined sources
Beta strandi76 – 783Combined sources
Beta strandi84 – 896Combined sources
Beta strandi90 – 923Combined sources
Helixi93 – 10614Combined sources
Turni107 – 1104Combined sources
Beta strandi111 – 1133Combined sources
Turni124 – 1263Combined sources
Beta strandi127 – 1326Combined sources
Beta strandi134 – 1374Combined sources
Beta strandi138 – 1403Combined sources
Helixi143 – 1453Combined sources
Beta strandi146 – 1483Combined sources
Beta strandi156 – 1583Combined sources
Helixi163 – 17210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NKWX-ray3.10D1-180[»]
1NWXX-ray3.50D1-180[»]
1NWYX-ray3.30D1-180[»]
1SM1X-ray3.42D1-180[»]
1XBPX-ray3.50D1-180[»]
2ZJPX-ray3.70D1-180[»]
2ZJQX-ray3.30D1-180[»]
2ZJRX-ray2.91D1-180[»]
3CF5X-ray3.30D1-180[»]
3DLLX-ray3.50D1-180[»]
3PIOX-ray3.25D1-180[»]
3PIPX-ray3.45D1-180[»]
4IO9X-ray3.20D1-180[»]
4IOAX-ray3.20D1-180[»]
4IOCX-ray3.60D1-180[»]
4U67X-ray3.65D1-180[»]
4V49X-ray8.70D2-179[»]
4V4AX-ray9.50D2-179[»]
4V4GX-ray11.50G2-179[»]
4WFNX-ray3.54D1-180[»]
5DM6X-ray2.90D3-179[»]
5DM7X-ray3.00D3-179[»]
ProteinModelPortaliQ9RXJ0.
SMRiQ9RXJ0. Positions 2-179.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RXJ0.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L5P family.Curated

Phylogenomic databases

eggNOGiENOG4105CW6. Bacteria.
COG0094. LUCA.
HOGENOMiHOG000231311.
InParanoidiQ9RXJ0.
KOiK02931.
OMAiEQVMFHE.
OrthoDBiEOG6M9F1R.

Family and domain databases

Gene3Di3.30.1440.10. 1 hit.
HAMAPiMF_01333_B. Ribosomal_L5_B.
InterProiIPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR031309. Ribosomal_L5_C.
IPR022803. Ribosomal_L5_domain.
IPR031310. Ribosomal_L5_N.
[Graphical view]
PfamiPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFiPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMiSSF55282. SSF55282. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9RXJ0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQQLKTKYND QVRPALMQQF GYSSVMAVPR IEKIVVNEGL GSSKEDSKAI
60 70 80 90 100
DKAAKELALI TLQKPIITKA KKSISNFKLR QGMPVGIKVT LRGERMYVFL
110 120 130 140 150
EKLINIGLPR IRDFRGINPN AFDGRGNYNL GIKEQLIFPE ITYDMVDKTR
160 170 180
GMDITIVTTA KTDEEARALL QSMGLPFRKQ
Length:180
Mass (Da):20,350
Last modified:May 1, 2000 - v1
Checksum:i755B760BA0E90F5B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09904.1.
PIRiC75535.
RefSeqiNP_294046.1. NC_001263.1.
WP_010886968.1. NC_001263.1.

Genome annotation databases

EnsemblBacteriaiAAF09904; AAF09904; DR_0323.
GeneIDi1798348.
KEGGidra:DR_0323.
PATRICi21628144. VBIDeiRad64572_0489.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09904.1.
PIRiC75535.
RefSeqiNP_294046.1. NC_001263.1.
WP_010886968.1. NC_001263.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NKWX-ray3.10D1-180[»]
1NWXX-ray3.50D1-180[»]
1NWYX-ray3.30D1-180[»]
1SM1X-ray3.42D1-180[»]
1XBPX-ray3.50D1-180[»]
2ZJPX-ray3.70D1-180[»]
2ZJQX-ray3.30D1-180[»]
2ZJRX-ray2.91D1-180[»]
3CF5X-ray3.30D1-180[»]
3DLLX-ray3.50D1-180[»]
3PIOX-ray3.25D1-180[»]
3PIPX-ray3.45D1-180[»]
4IO9X-ray3.20D1-180[»]
4IOAX-ray3.20D1-180[»]
4IOCX-ray3.60D1-180[»]
4U67X-ray3.65D1-180[»]
4V49X-ray8.70D2-179[»]
4V4AX-ray9.50D2-179[»]
4V4GX-ray11.50G2-179[»]
4WFNX-ray3.54D1-180[»]
5DM6X-ray2.90D3-179[»]
5DM7X-ray3.00D3-179[»]
ProteinModelPortaliQ9RXJ0.
SMRiQ9RXJ0. Positions 2-179.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0323.

Proteomic databases

PRIDEiQ9RXJ0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF09904; AAF09904; DR_0323.
GeneIDi1798348.
KEGGidra:DR_0323.
PATRICi21628144. VBIDeiRad64572_0489.

Phylogenomic databases

eggNOGiENOG4105CW6. Bacteria.
COG0094. LUCA.
HOGENOMiHOG000231311.
InParanoidiQ9RXJ0.
KOiK02931.
OMAiEQVMFHE.
OrthoDBiEOG6M9F1R.

Enzyme and pathway databases

BioCyciDRAD243230:GH46-333-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9RXJ0.

Family and domain databases

Gene3Di3.30.1440.10. 1 hit.
HAMAPiMF_01333_B. Ribosomal_L5_B.
InterProiIPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR031309. Ribosomal_L5_C.
IPR022803. Ribosomal_L5_domain.
IPR031310. Ribosomal_L5_N.
[Graphical view]
PfamiPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFiPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMiSSF55282. SSF55282. 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. "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.
  3. "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.
  4. "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.
  5. "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.
  6. "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.
  7. "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.
  8. "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 nameiRL5_DEIRA
AccessioniPrimary (citable) accession number: Q9RXJ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: May 1, 2000
Last modified: February 17, 2016
This is version 100 of the entry and version 1 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.