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Q5SHQ0

- RL5_THET8

UniProt

Q5SHQ0 - RL5_THET8

Protein

50S ribosomal protein L5

Gene

rplE

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    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

    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: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. ribosome Source: UniProtKB-KW

    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 – 127
    Helixi15 – 239
    Turni28 – 303
    Beta strandi34 – 418
    Helixi44 – 463
    Beta strandi47 – 504
    Helixi55 – 6410
    Beta strandi69 – 757
    Beta strandi78 – 814
    Beta strandi84 – 9411
    Helixi96 – 10813
    Helixi110 – 1134
    Beta strandi114 – 1163
    Beta strandi118 – 1203
    Helixi122 – 1243
    Beta strandi127 – 13610
    Helixi138 – 1403
    Beta strandi141 – 1433
    Beta strandi146 – 1483
    Beta strandi155 – 1628
    Helixi166 – 1749
    Turni175 – 1773

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GIYX-ray5.50G1-182[»]
    1YL3X-ray5.50G32-38[»]
    2HGJX-ray5.00G1-182[»]
    2HGQX-ray5.50G1-182[»]
    2HGUX-ray4.51G1-182[»]
    2J01X-ray2.80G2-182[»]
    2J03X-ray2.80G2-182[»]
    2V47X-ray3.50G2-182[»]
    2V49X-ray3.50G2-182[»]
    2WDIX-ray3.30G1-182[»]
    2WDJX-ray3.30G1-182[»]
    2WDLX-ray3.50G1-182[»]
    2WDNX-ray3.50G1-182[»]
    2WH2X-ray3.45G1-182[»]
    2WH4X-ray3.45G1-182[»]
    2WRJX-ray3.60G1-182[»]
    2WRLX-ray3.60G1-182[»]
    2WROX-ray3.60G1-182[»]
    2WRRX-ray3.60G1-182[»]
    2X9SX-ray3.10G1-182[»]
    2X9UX-ray3.10G1-182[»]
    2XG0X-ray3.20G1-182[»]
    2XG2X-ray3.20G1-182[»]
    2XQEX-ray3.10G1-182[»]
    2XTGelectron microscopy7.80G1-182[»]
    2XUXelectron microscopy7.60G1-182[»]
    2Y0VX-ray3.10G1-182[»]
    2Y0XX-ray3.10G1-182[»]
    2Y0ZX-ray3.10G1-182[»]
    2Y11X-ray3.10G1-182[»]
    2Y13X-ray3.10G1-182[»]
    2Y15X-ray3.10G1-182[»]
    2Y17X-ray3.10G1-182[»]
    2Y19X-ray3.10G1-182[»]
    3FINelectron microscopy6.40G2-182[»]
    3HUXX-ray3.10G1-182[»]
    3HUZX-ray3.10G1-182[»]
    3I8FX-ray3.10G1-182[»]
    3I8IX-ray3.10G1-182[»]
    3I9CX-ray3.50G1-182[»]
    3I9EX-ray3.50G1-182[»]
    3KIRX-ray3.30G1-182[»]
    3KITX-ray3.30G1-182[»]
    3KIWX-ray3.60G1-182[»]
    3KIYX-ray3.60G1-182[»]
    3KNIX-ray3.00G1-182[»]
    3KNKX-ray3.00G1-182[»]
    3KNMX-ray3.45G1-182[»]
    3KNOX-ray3.45G1-182[»]
    3TVEX-ray3.10G2-182[»]
    3TVHX-ray3.10G2-182[»]
    3UXQX-ray3.20G1-182[»]
    3UXRX-ray3.20G1-182[»]
    3UYEX-ray3.00G1-182[»]
    3UYGX-ray3.00G1-182[»]
    3UZ1X-ray3.30G1-182[»]
    3UZ2X-ray3.30G1-182[»]
    3UZ8X-ray3.00G1-182[»]
    3UZ9X-ray3.00G1-182[»]
    3UZFX-ray3.30G1-182[»]
    3UZHX-ray3.30G1-182[»]
    3UZKX-ray3.30G1-182[»]
    3UZNX-ray3.30G1-182[»]
    3V23X-ray3.00G1-182[»]
    3V25X-ray3.00G1-182[»]
    3V27X-ray3.10G1-182[»]
    3V29X-ray3.10G1-182[»]
    3V2DX-ray2.70G1-182[»]
    3V2FX-ray2.70G1-182[»]
    3V6WX-ray3.90G1-182[»]
    3V6XX-ray3.90G1-182[»]
    3ZN9X-ray3.10G1-182[»]
    3ZNEX-ray3.10G1-182[»]
    3ZVPX-ray3.80G1-182[»]
    4ABSX-ray3.10G1-182[»]
    4B8GX-ray3.70G1-182[»]
    4B8IX-ray3.70G1-182[»]
    4BTDX-ray2.95G2-182[»]
    4BYCX-ray3.35G1-182[»]
    4BYEX-ray3.35G1-182[»]
    4DHAX-ray3.20G1-182[»]
    4DHCX-ray3.20G1-182[»]
    4EJBX-ray3.52G1-182[»]
    4EJCX-ray3.52G1-182[»]
    4G5LX-ray3.30G1-182[»]
    4G5NX-ray3.30G1-182[»]
    4G5UX-ray3.10G1-182[»]
    4G5WX-ray3.10G1-182[»]
    4JUXX-ray2.86G1-182[»]
    4K0MX-ray3.30G2-182[»]
    4K0QX-ray3.30G2-182[»]
    4NVVX-ray3.00G1-182[»]
    4NVXX-ray3.00G1-182[»]
    4NVZX-ray3.10G1-182[»]
    4NW1X-ray3.10G1-182[»]
    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.
    OMAiTEQLIFP.
    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

    MPLDVALKRK YYEEVRPELI RRFGYQNVWE VPRLEKVVIN QGLGEAKEDA    50
    RILEKAAQEL ALITGQKPAV TRAKKSISNF KLRKGMPIGL RVTLRRDRMW 100
    IFLEKLLNVA LPRIRDFRGL NPNSFDGRGN YNLGLREQLI FPEITYDMVD 150
    ALRGMDIAVV TTAETDEEAR ALLELLGFPF RK 182
    Length:182
    Mass (Da):21,030
    Last modified:January 23, 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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008226 Genomic DNA. Translation: BAD71503.1.
    RefSeqiWP_011228843.1. NC_006461.1.
    YP_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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008226 Genomic DNA. Translation: BAD71503.1 .
    RefSeqi WP_011228843.1. NC_006461.1.
    YP_144946.1. NC_006461.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1GIY X-ray 5.50 G 1-182 [» ]
    1YL3 X-ray 5.50 G 32-38 [» ]
    2HGJ X-ray 5.00 G 1-182 [» ]
    2HGQ X-ray 5.50 G 1-182 [» ]
    2HGU X-ray 4.51 G 1-182 [» ]
    2J01 X-ray 2.80 G 2-182 [» ]
    2J03 X-ray 2.80 G 2-182 [» ]
    2V47 X-ray 3.50 G 2-182 [» ]
    2V49 X-ray 3.50 G 2-182 [» ]
    2WDI X-ray 3.30 G 1-182 [» ]
    2WDJ X-ray 3.30 G 1-182 [» ]
    2WDL X-ray 3.50 G 1-182 [» ]
    2WDN X-ray 3.50 G 1-182 [» ]
    2WH2 X-ray 3.45 G 1-182 [» ]
    2WH4 X-ray 3.45 G 1-182 [» ]
    2WRJ X-ray 3.60 G 1-182 [» ]
    2WRL X-ray 3.60 G 1-182 [» ]
    2WRO X-ray 3.60 G 1-182 [» ]
    2WRR X-ray 3.60 G 1-182 [» ]
    2X9S X-ray 3.10 G 1-182 [» ]
    2X9U X-ray 3.10 G 1-182 [» ]
    2XG0 X-ray 3.20 G 1-182 [» ]
    2XG2 X-ray 3.20 G 1-182 [» ]
    2XQE X-ray 3.10 G 1-182 [» ]
    2XTG electron microscopy 7.80 G 1-182 [» ]
    2XUX electron microscopy 7.60 G 1-182 [» ]
    2Y0V X-ray 3.10 G 1-182 [» ]
    2Y0X X-ray 3.10 G 1-182 [» ]
    2Y0Z X-ray 3.10 G 1-182 [» ]
    2Y11 X-ray 3.10 G 1-182 [» ]
    2Y13 X-ray 3.10 G 1-182 [» ]
    2Y15 X-ray 3.10 G 1-182 [» ]
    2Y17 X-ray 3.10 G 1-182 [» ]
    2Y19 X-ray 3.10 G 1-182 [» ]
    3FIN electron microscopy 6.40 G 2-182 [» ]
    3HUX X-ray 3.10 G 1-182 [» ]
    3HUZ X-ray 3.10 G 1-182 [» ]
    3I8F X-ray 3.10 G 1-182 [» ]
    3I8I X-ray 3.10 G 1-182 [» ]
    3I9C X-ray 3.50 G 1-182 [» ]
    3I9E X-ray 3.50 G 1-182 [» ]
    3KIR X-ray 3.30 G 1-182 [» ]
    3KIT X-ray 3.30 G 1-182 [» ]
    3KIW X-ray 3.60 G 1-182 [» ]
    3KIY X-ray 3.60 G 1-182 [» ]
    3KNI X-ray 3.00 G 1-182 [» ]
    3KNK X-ray 3.00 G 1-182 [» ]
    3KNM X-ray 3.45 G 1-182 [» ]
    3KNO X-ray 3.45 G 1-182 [» ]
    3TVE X-ray 3.10 G 2-182 [» ]
    3TVH X-ray 3.10 G 2-182 [» ]
    3UXQ X-ray 3.20 G 1-182 [» ]
    3UXR X-ray 3.20 G 1-182 [» ]
    3UYE X-ray 3.00 G 1-182 [» ]
    3UYG X-ray 3.00 G 1-182 [» ]
    3UZ1 X-ray 3.30 G 1-182 [» ]
    3UZ2 X-ray 3.30 G 1-182 [» ]
    3UZ8 X-ray 3.00 G 1-182 [» ]
    3UZ9 X-ray 3.00 G 1-182 [» ]
    3UZF X-ray 3.30 G 1-182 [» ]
    3UZH X-ray 3.30 G 1-182 [» ]
    3UZK X-ray 3.30 G 1-182 [» ]
    3UZN X-ray 3.30 G 1-182 [» ]
    3V23 X-ray 3.00 G 1-182 [» ]
    3V25 X-ray 3.00 G 1-182 [» ]
    3V27 X-ray 3.10 G 1-182 [» ]
    3V29 X-ray 3.10 G 1-182 [» ]
    3V2D X-ray 2.70 G 1-182 [» ]
    3V2F X-ray 2.70 G 1-182 [» ]
    3V6W X-ray 3.90 G 1-182 [» ]
    3V6X X-ray 3.90 G 1-182 [» ]
    3ZN9 X-ray 3.10 G 1-182 [» ]
    3ZNE X-ray 3.10 G 1-182 [» ]
    3ZVP X-ray 3.80 G 1-182 [» ]
    4ABS X-ray 3.10 G 1-182 [» ]
    4B8G X-ray 3.70 G 1-182 [» ]
    4B8I X-ray 3.70 G 1-182 [» ]
    4BTD X-ray 2.95 G 2-182 [» ]
    4BYC X-ray 3.35 G 1-182 [» ]
    4BYE X-ray 3.35 G 1-182 [» ]
    4DHA X-ray 3.20 G 1-182 [» ]
    4DHC X-ray 3.20 G 1-182 [» ]
    4EJB X-ray 3.52 G 1-182 [» ]
    4EJC X-ray 3.52 G 1-182 [» ]
    4G5L X-ray 3.30 G 1-182 [» ]
    4G5N X-ray 3.30 G 1-182 [» ]
    4G5U X-ray 3.10 G 1-182 [» ]
    4G5W X-ray 3.10 G 1-182 [» ]
    4JUX X-ray 2.86 G 1-182 [» ]
    4K0M X-ray 3.30 G 2-182 [» ]
    4K0Q X-ray 3.30 G 2-182 [» ]
    4NVV X-ray 3.00 G 1-182 [» ]
    4NVX X-ray 3.00 G 1-182 [» ]
    4NVZ X-ray 3.10 G 1-182 [» ]
    4NW1 X-ray 3.10 G 1-182 [» ]
    ProteinModelPortali Q5SHQ0.
    SMRi Q5SHQ0. Positions 1-182.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 300852.TTHA1680.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD71503 ; BAD71503 ; BAD71503 .
    GeneIDi 3169803.
    KEGGi ttj:TTHA1680.
    PATRICi 23958315. VBITheThe93045_1650.

    Phylogenomic databases

    eggNOGi COG0094.
    HOGENOMi HOG000231311.
    KOi K02931.
    OMAi TEQLIFP.
    OrthoDBi EOG6M9F1R.
    PhylomeDBi Q5SHQ0.

    Enzyme and pathway databases

    BioCyci TTHE300852:GH8R-1719-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q5SHQ0.

    Family and domain databases

    Gene3Di 3.30.1440.10. 1 hit.
    HAMAPi MF_01333_B. Ribosomal_L5_B.
    InterProi IPR002132. Ribosomal_L5.
    IPR020930. Ribosomal_L5_bac-type.
    IPR020929. Ribosomal_L5_CS.
    IPR022803. Ribosomal_L5_domain.
    [Graphical view ]
    PANTHERi PTHR11994. PTHR11994. 1 hit.
    Pfami PF00281. Ribosomal_L5. 1 hit.
    PF00673. Ribosomal_L5_C. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF002161. Ribosomal_L5. 1 hit.
    SUPFAMi SSF55282. SSF55282. 1 hit.
    PROSITEi PS00358. RIBOSOMAL_L5. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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(1991) [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 (NOV-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(1996)
      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(1995)
      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(2000) [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(2005) [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(2001) [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 29, 2005
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 92 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 1 Publication 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