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Protein

50S ribosomal protein L5

Gene

rplE

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 4 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 (forming bridge B1b) connecting the head of the 30S subunit to the top of the 50S subunit. The bridge itself contacts the P site tRNA and is implicated in movement during ribosome translocation. Also contacts the P site tRNA independently of the intersubunit bridge; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.

GO - Molecular functioni

  1. rRNA binding Source: UniProtKB-HAMAP
  2. structural constituent of ribosome Source: InterPro
  3. tRNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding, tRNA-binding

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-1719-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L5
Gene namesi
Name:rplE
Ordered Locus Names:TTHA1680
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000532 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. ribosome Source: UniProtKB-KW
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed3 Publications
Chaini2 – 18218150S ribosomal protein L5PRO_0000125014Add
BLAST

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 (TL5) subcomplex; has also been isolated as a complex with 5S rRNA, RL25 (TL5) and DNA binding protein II. Forms a bridge to the 30S subunit in the 70S ribosome, contacting protein S13; this bridge is straddled by the 5S rRNA. Contacts the P site tRNA.

Protein-protein interaction databases

STRINGi300852.TTHA1680.

Structurei

Secondary structure

1
182
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 138Combined sources
Helixi15 – 239Combined sources
Turni28 – 303Combined sources
Beta strandi34 – 418Combined sources
Helixi44 – 463Combined sources
Beta strandi47 – 515Combined sources
Helixi54 – 6411Combined sources
Beta strandi69 – 724Combined sources
Beta strandi74 – 763Combined sources
Turni78 – 814Combined sources
Beta strandi83 – 864Combined sources
Beta strandi87 – 948Combined sources
Helixi96 – 10813Combined sources
Helixi110 – 1134Combined sources
Beta strandi114 – 1163Combined sources
Beta strandi118 – 1203Combined sources
Helixi122 – 1243Combined sources
Beta strandi127 – 13610Combined sources
Helixi138 – 1403Combined sources
Beta strandi141 – 1433Combined sources
Helixi146 – 1483Combined sources
Beta strandi155 – 1628Combined sources
Helixi166 – 17611Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VVJX-ray3.44RG/YG1-182[»]
1VY4X-ray2.60BG/DG1-182[»]
1VY5X-ray2.55BG/DG1-182[»]
1VY6X-ray2.90BG/DG1-182[»]
1VY7X-ray2.80BG/DG1-182[»]
4L47X-ray3.22RG/YG1-182[»]
4L71X-ray3.90RG/YG1-182[»]
4LELX-ray3.90RG/YG1-182[»]
4LFZX-ray3.92RG/YG1-182[»]
4LNTX-ray2.94RG/YG1-182[»]
4LSKX-ray3.48RG/YG1-182[»]
4LT8X-ray3.14RG/YG1-182[»]
4P6FX-ray3.60RG/YG1-182[»]
4P70X-ray3.68RG/YG1-182[»]
4V42X-ray5.50RG1-182[»]
4V4PX-ray5.50G32-38[»]
4V4XX-ray5.00G1-182[»]
4V4YX-ray5.50G1-182[»]
4V4ZX-ray4.51G1-182[»]
4V51X-ray2.80BG/DG2-182[»]
4V5AX-ray3.50BG/DG2-182[»]
4V5CX-ray3.30BG/DG1-182[»]
4V5DX-ray3.50BG/DG1-182[»]
4V5EX-ray3.45BG/DG1-182[»]
4V5FX-ray3.60BG/DG1-182[»]
4V5GX-ray3.60BG/DG1-182[»]
4V5JX-ray3.10BG/DG1-182[»]
4V5KX-ray3.20BG/DG1-182[»]
4V5LX-ray3.10BG1-182[»]
4V5Melectron microscopy7.80BG1-182[»]
4V5Nelectron microscopy7.60BG1-182[»]
4V5PX-ray3.10BG/DG1-182[»]
4V5QX-ray3.10BG/DG1-182[»]
4V5RX-ray3.10BG/DG1-182[»]
4V5SX-ray3.10BG/DG1-182[»]
4V68electron microscopy6.40BG2-182[»]
4V6AX-ray3.10BG/DG1-182[»]
4V6FX-ray3.10AG/DG1-182[»]
4V6GX-ray3.50BG/DG1-182[»]
4V7JX-ray3.30AG/BG1-182[»]
4V7KX-ray3.60AG/BG1-182[»]
4V7LX-ray3.00BG/DG1-182[»]
4V7MX-ray3.45BG/DG1-182[»]
4V7WX-ray3.00BG/DG1-182[»]
4V7XX-ray3.00BG/DG1-182[»]
4V7YX-ray3.00BG/DG1-182[»]
4V7ZX-ray3.10BG/DG1-182[»]
4V87X-ray3.10AG/DG2-182[»]
4V8AX-ray3.20AG/BG1-182[»]
4V8BX-ray3.00BG/DG1-182[»]
4V8CX-ray3.30AG/BG1-182[»]
4V8DX-ray3.00BG/DG1-182[»]
4V8EX-ray3.30AG/CG1-182[»]
4V8FX-ray3.30AG/DG1-182[»]
4V8GX-ray3.00BG/DG1-182[»]
4V8HX-ray3.10BG/DG1-182[»]
4V8IX-ray2.70BG/DG1-182[»]
4V8JX-ray3.90BG/DG1-182[»]
4V8NX-ray3.10BG/DG1-182[»]
4V8OX-ray3.80BG1-182[»]
4V8QX-ray3.10AG1-182[»]
4V8UX-ray3.70BG/DG1-182[»]
4V8XX-ray3.35BG/DG1-182[»]
4V90X-ray2.95BG2-182[»]
4V95X-ray3.20BG/DG1-182[»]
4V97X-ray3.52BG/DG1-182[»]
4V9AX-ray3.30BG/DG1-182[»]
4V9BX-ray3.10BG/DG1-182[»]
4V9HX-ray2.86BG1-182[»]
4V9IX-ray3.30BG/DG2-182[»]
4V9RX-ray3.00BG/DG1-182[»]
4V9SX-ray3.10BG/DG1-182[»]
4W2EX-ray2.90G1-182[»]
4W2FX-ray2.40BG/DG1-182[»]
4W2GX-ray2.55BG/DG1-182[»]
4W2HX-ray2.70BG/DG1-182[»]
4W2IX-ray2.70BG/DG1-182[»]
ProteinModelPortaliQ5SHQ0.
SMRiQ5SHQ0. Positions 1-182.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SHQ0.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L5P family.Curated

Phylogenomic databases

eggNOGiCOG0094.
HOGENOMiHOG000231311.
KOiK02931.
OMAiEQVMFHE.
OrthoDBiEOG6M9F1R.
PhylomeDBiQ5SHQ0.

Family and domain databases

Gene3Di3.30.1440.10. 1 hit.
HAMAPiMF_01333_B. Ribosomal_L5_B.
InterProiIPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR020929. Ribosomal_L5_CS.
IPR022803. Ribosomal_L5_domain.
[Graphical view]
PANTHERiPTHR11994. PTHR11994. 1 hit.
PfamiPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFiPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMiSSF55282. SSF55282. 1 hit.
PROSITEiPS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q5SHQ0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPLDVALKRK YYEEVRPELI RRFGYQNVWE VPRLEKVVIN QGLGEAKEDA
60 70 80 90 100
RILEKAAQEL ALITGQKPAV TRAKKSISNF KLRKGMPIGL RVTLRRDRMW
110 120 130 140 150
IFLEKLLNVA LPRIRDFRGL NPNSFDGRGN YNLGLREQLI FPEITYDMVD
160 170 180
ALRGMDIAVV TTAETDEEAR ALLELLGFPF RK
Length:182
Mass (Da):21,030
Last modified:January 22, 2007 - v3
Checksum:i69A3361F6825929B
GO

Mass spectrometryi

Molecular mass is 20900 Da from positions 2 - 182. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD71503.1.
RefSeqiYP_144946.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71503; BAD71503; BAD71503.
GeneIDi3169803.
KEGGittj:TTHA1680.
PATRICi23958315. VBITheThe93045_1650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD71503.1.
RefSeqiYP_144946.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VVJX-ray3.44RG/YG1-182[»]
1VY4X-ray2.60BG/DG1-182[»]
1VY5X-ray2.55BG/DG1-182[»]
1VY6X-ray2.90BG/DG1-182[»]
1VY7X-ray2.80BG/DG1-182[»]
4L47X-ray3.22RG/YG1-182[»]
4L71X-ray3.90RG/YG1-182[»]
4LELX-ray3.90RG/YG1-182[»]
4LFZX-ray3.92RG/YG1-182[»]
4LNTX-ray2.94RG/YG1-182[»]
4LSKX-ray3.48RG/YG1-182[»]
4LT8X-ray3.14RG/YG1-182[»]
4P6FX-ray3.60RG/YG1-182[»]
4P70X-ray3.68RG/YG1-182[»]
4V42X-ray5.50RG1-182[»]
4V4PX-ray5.50G32-38[»]
4V4XX-ray5.00G1-182[»]
4V4YX-ray5.50G1-182[»]
4V4ZX-ray4.51G1-182[»]
4V51X-ray2.80BG/DG2-182[»]
4V5AX-ray3.50BG/DG2-182[»]
4V5CX-ray3.30BG/DG1-182[»]
4V5DX-ray3.50BG/DG1-182[»]
4V5EX-ray3.45BG/DG1-182[»]
4V5FX-ray3.60BG/DG1-182[»]
4V5GX-ray3.60BG/DG1-182[»]
4V5JX-ray3.10BG/DG1-182[»]
4V5KX-ray3.20BG/DG1-182[»]
4V5LX-ray3.10BG1-182[»]
4V5Melectron microscopy7.80BG1-182[»]
4V5Nelectron microscopy7.60BG1-182[»]
4V5PX-ray3.10BG/DG1-182[»]
4V5QX-ray3.10BG/DG1-182[»]
4V5RX-ray3.10BG/DG1-182[»]
4V5SX-ray3.10BG/DG1-182[»]
4V68electron microscopy6.40BG2-182[»]
4V6AX-ray3.10BG/DG1-182[»]
4V6FX-ray3.10AG/DG1-182[»]
4V6GX-ray3.50BG/DG1-182[»]
4V7JX-ray3.30AG/BG1-182[»]
4V7KX-ray3.60AG/BG1-182[»]
4V7LX-ray3.00BG/DG1-182[»]
4V7MX-ray3.45BG/DG1-182[»]
4V7WX-ray3.00BG/DG1-182[»]
4V7XX-ray3.00BG/DG1-182[»]
4V7YX-ray3.00BG/DG1-182[»]
4V7ZX-ray3.10BG/DG1-182[»]
4V87X-ray3.10AG/DG2-182[»]
4V8AX-ray3.20AG/BG1-182[»]
4V8BX-ray3.00BG/DG1-182[»]
4V8CX-ray3.30AG/BG1-182[»]
4V8DX-ray3.00BG/DG1-182[»]
4V8EX-ray3.30AG/CG1-182[»]
4V8FX-ray3.30AG/DG1-182[»]
4V8GX-ray3.00BG/DG1-182[»]
4V8HX-ray3.10BG/DG1-182[»]
4V8IX-ray2.70BG/DG1-182[»]
4V8JX-ray3.90BG/DG1-182[»]
4V8NX-ray3.10BG/DG1-182[»]
4V8OX-ray3.80BG1-182[»]
4V8QX-ray3.10AG1-182[»]
4V8UX-ray3.70BG/DG1-182[»]
4V8XX-ray3.35BG/DG1-182[»]
4V90X-ray2.95BG2-182[»]
4V95X-ray3.20BG/DG1-182[»]
4V97X-ray3.52BG/DG1-182[»]
4V9AX-ray3.30BG/DG1-182[»]
4V9BX-ray3.10BG/DG1-182[»]
4V9HX-ray2.86BG1-182[»]
4V9IX-ray3.30BG/DG2-182[»]
4V9RX-ray3.00BG/DG1-182[»]
4V9SX-ray3.10BG/DG1-182[»]
4W2EX-ray2.90G1-182[»]
4W2FX-ray2.40BG/DG1-182[»]
4W2GX-ray2.55BG/DG1-182[»]
4W2HX-ray2.70BG/DG1-182[»]
4W2IX-ray2.70BG/DG1-182[»]
ProteinModelPortaliQ5SHQ0.
SMRiQ5SHQ0. Positions 1-182.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1680.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71503; BAD71503; BAD71503.
GeneIDi3169803.
KEGGittj:TTHA1680.
PATRICi23958315. VBITheThe93045_1650.

Phylogenomic databases

eggNOGiCOG0094.
HOGENOMiHOG000231311.
KOiK02931.
OMAiEQVMFHE.
OrthoDBiEOG6M9F1R.
PhylomeDBiQ5SHQ0.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-1719-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5SHQ0.

Family and domain databases

Gene3Di3.30.1440.10. 1 hit.
HAMAPiMF_01333_B. Ribosomal_L5_B.
InterProiIPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR020929. Ribosomal_L5_CS.
IPR022803. Ribosomal_L5_domain.
[Graphical view]
PANTHERiPTHR11994. PTHR11994. 1 hit.
PfamiPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFiPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMiSSF55282. SSF55282. 1 hit.
PROSITEiPS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Comparative analysis of ribosomal protein L5 sequences from bacteria of the genus Thermus."
    Jahn O., Hartmann R.K., Boeckh T., Erdmann V.A.
    Biochimie 73:669-678(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  3. "Identification, purification and partial sequence of four Thermus thermophilus 5S rRNA binding proteins."
    Kim J.-S., Boysen R.I., Schroeder W., Erdmann V.A., Gessner R.V.
    Endocyt. Cell Res. 11:177-194(1995)
    Cited for: PROTEIN SEQUENCE OF 2-44, ISOLATION OF 5S RRNA-ASSOCIATED COMPLEXES.
  4. "The isolation and complete amino acid sequence of the ribosomal protein L36 from Thermus thermophilus and its zinc-binding motif."
    Boysen R.I., Lorenz S., Kim J.S., Schroeder W.F.K.J., Erdmann V.A.
    Endocyt. Cell Res. 11:41-58(1994)
    Cited for: PROTEIN SEQUENCE OF 2-41.
  5. "Identification of the 50S ribosomal proteins from the eubacterium Thermus thermophilus."
    Katsani K.R., Tsiboli P., Anagnostopoulos K., Urlaub H., Choli-Papadopoulou T.
    Biol. Chem. 381:1079-1087(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-28.
  6. "Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry."
    Suh M.-J., Hamburg D.M., Gregory S.T., Dahlberg A.E., Limbach P.A.
    Proteomics 5:4818-4831(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY.
  7. "The path of messenger RNA through the ribosome."
    Yusupova G.Z., Yusupov M.M., Cate J.H.D., Noller H.F.
    Cell 106:233-241(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (5.0 ANGSTROMS) OF THE RIBOSOME.
  8. Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME, INTERSUBUNIT BRIDGE FORMATION.

Entry informationi

Entry nameiRL5_THET8
AccessioniPrimary (citable) accession number: Q5SHQ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 28, 2005
Last sequence update: January 22, 2007
Last modified: March 31, 2015
This is version 98 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Note that in Ref. 3 it was shown that the initiator methionine is not removed, in PubMed:11154066 it was shown the initiator methionine is removed, and the mass determined in PubMed:16287167 is compatible with initiator methionine removal.Curated
In PubMed:11154066 there is uncertainty about the number of Arg residues at position 10 and whether position 25 is Pro or Tyr.Curated

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

External Data

Dasty 3

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 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.