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Q5SHZ1

- RL25_THET8

UniProt

Q5SHZ1 - RL25_THET8

Protein

50S ribosomal protein L25

Gene

rplY

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 86 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
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    Functioni

    This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit.

    GO - Molecular functioni

    1. 5S rRNA binding Source: InterPro
    2. structural constituent of ribosome Source: InterPro

    GO - Biological processi

    1. translation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Keywords - Ligandi

    RNA-binding, rRNA-binding

    Enzyme and pathway databases

    BioCyciTTHE300852:GH8R-1628-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    50S ribosomal protein L25
    Short name:
    TL5
    Gene namesi
    Name:rplY
    Synonyms:rpl25, rptL5
    Ordered Locus Names:TTHA1589
    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
    Chaini1 – 20620650S ribosomal protein L25PRO_0000181608Add
    BLAST

    Interactioni

    Subunit structurei

    Part of the 50S ribosomal subunit. Contacts the 5S rRNA; has been isolated in a complex with 5S rRNA and RL5, 5S rRNA and DNA binding protein II; 5S rRNA and RL18; 5S rRNA, RL5 and DNA binding protein II (PubMed:16287167).

    Protein-protein interaction databases

    STRINGi300852.TTHA1589.

    Structurei

    Secondary structure

    1
    206
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 97
    Beta strandi11 – 133
    Helixi15 – 206
    Beta strandi23 – 308
    Beta strandi33 – 408
    Helixi41 – 5111
    Turni52 – 543
    Beta strandi57 – 604
    Beta strandi62 – 643
    Beta strandi66 – 7712
    Turni78 – 814
    Beta strandi82 – 909
    Beta strandi92 – 943
    Beta strandi96 – 1016
    Beta strandi103 – 1064
    Turni107 – 1093
    Turni111 – 1144
    Beta strandi116 – 1183
    Beta strandi122 – 1287
    Beta strandi130 – 1323
    Beta strandi138 – 1403
    Beta strandi142 – 1443
    Beta strandi145 – 1473
    Beta strandi148 – 1503
    Beta strandi152 – 1543
    Beta strandi159 – 1635
    Beta strandi167 – 1693
    Beta strandi172 – 1754
    Helixi180 – 1823
    Helixi183 – 1864
    Beta strandi188 – 1958
    Beta strandi199 – 2013

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GIYX-ray5.50V1-206[»]
    2HGJX-ray5.00Y1-206[»]
    2HGQX-ray5.50Y1-206[»]
    2HGUX-ray4.51Y1-206[»]
    2J01X-ray2.80Z1-206[»]
    2J03X-ray2.80Z1-206[»]
    2V47X-ray3.80Z1-206[»]
    2V49X-ray3.80Z1-206[»]
    2WDIX-ray3.30Z1-206[»]
    2WDJX-ray3.30Z1-206[»]
    2WDLX-ray3.50Z1-206[»]
    2WDNX-ray3.50Z1-206[»]
    2WH2X-ray3.45Z1-206[»]
    2WH4X-ray3.45Z1-206[»]
    2WRJX-ray3.60Z1-206[»]
    2WRLX-ray3.60Z1-206[»]
    2WROX-ray3.60Z1-206[»]
    2WRRX-ray3.60Z1-206[»]
    2X9SX-ray3.10Z1-206[»]
    2X9UX-ray3.10Z1-206[»]
    2XG0X-ray3.20Z1-206[»]
    2XG2X-ray3.20Z1-206[»]
    2XQEX-ray3.10Z1-206[»]
    2XTGelectron microscopy7.80Z1-206[»]
    2XUXelectron microscopy7.60Z1-206[»]
    2Y0VX-ray3.10Z1-206[»]
    2Y0XX-ray3.10Z1-206[»]
    2Y0ZX-ray3.10Z1-206[»]
    2Y11X-ray3.10Z1-206[»]
    2Y13X-ray3.10Z1-206[»]
    2Y15X-ray3.10Z1-206[»]
    2Y17X-ray3.10Z1-206[»]
    2Y19X-ray3.10Z1-206[»]
    3FINelectron microscopy6.40Z3-179[»]
    3HUXX-ray3.10Z1-206[»]
    3HUZX-ray3.10Z1-206[»]
    3I8FX-ray3.10V1-206[»]
    3I8IX-ray3.10V1-206[»]
    3I9CX-ray3.50V1-206[»]
    3I9EX-ray3.50V1-206[»]
    3KIRX-ray3.30Z1-206[»]
    3KITX-ray3.30Z1-206[»]
    3KIWX-ray3.60Z1-206[»]
    3KIYX-ray3.60Z1-206[»]
    3KNIX-ray3.00Z1-206[»]
    3KNKX-ray3.00Z1-206[»]
    3KNMX-ray3.45Z1-206[»]
    3KNOX-ray3.45Z1-206[»]
    3TVEX-ray3.10V1-175[»]
    3TVHX-ray3.10V1-179[»]
    3UXQX-ray3.20Z1-206[»]
    3UXRX-ray3.20Z1-206[»]
    3UYEX-ray3.00V1-206[»]
    3UYGX-ray3.00V1-206[»]
    3UZ1X-ray3.30V1-206[»]
    3UZ2X-ray3.30V1-206[»]
    3UZ8X-ray3.00V1-206[»]
    3UZ9X-ray3.00V1-206[»]
    3UZFX-ray3.30V1-206[»]
    3UZHX-ray3.30V1-206[»]
    3UZKX-ray3.30V1-206[»]
    3UZNX-ray3.30V1-206[»]
    3V23X-ray3.00Z1-206[»]
    3V25X-ray3.00Z1-206[»]
    3V27X-ray3.10Z1-206[»]
    3V29X-ray3.10Z1-206[»]
    3V2DX-ray2.70Z1-206[»]
    3V2FX-ray2.70Z1-206[»]
    3V6WX-ray3.90Z1-206[»]
    3V6XX-ray3.90Z1-206[»]
    3ZN9X-ray3.10Z1-206[»]
    3ZNEX-ray3.10Z1-206[»]
    3ZVPX-ray3.80Z1-206[»]
    4ABSX-ray3.10Z1-206[»]
    4B8GX-ray3.70Z1-206[»]
    4B8IX-ray3.70Z1-206[»]
    4BTDX-ray2.95Z2-206[»]
    4BYCX-ray3.35Z1-206[»]
    4BYEX-ray3.35Z1-206[»]
    4DHAX-ray3.20Z1-206[»]
    4DHCX-ray3.20Z1-206[»]
    4EJBX-ray3.52Z1-206[»]
    4EJCX-ray3.52Z1-206[»]
    4G5LX-ray3.30V1-206[»]
    4G5NX-ray3.30V1-206[»]
    4G5UX-ray3.10V1-206[»]
    4G5WX-ray3.10V1-206[»]
    4JUXX-ray2.86Z1-206[»]
    4K0MX-ray3.30Z3-178[»]
    4K0QX-ray3.30Z3-178[»]
    4NVVX-ray3.00Z1-206[»]
    4NVXX-ray3.00Z1-206[»]
    4NVZX-ray3.10Z1-206[»]
    4NW1X-ray3.10Z1-206[»]
    ProteinModelPortaliQ5SHZ1.
    SMRiQ5SHZ1. Positions 1-185.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SHZ1.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1825.
    HOGENOMiHOG000214906.
    KOiK02897.
    OMAiCIGVKLG.
    OrthoDBiEOG6SZ1PC.
    PhylomeDBiQ5SHZ1.

    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.
    IPR011035. Ribosomal_L25/Gln-tRNA_synth.
    IPR020057. Ribosomal_L25_b-dom.
    IPR001021. Ribosomal_L25_long.
    [Graphical view]
    PfamiPF14693. Ribosomal_TL5_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF50715. SSF50715. 1 hit.
    TIGRFAMsiTIGR00731. ctc_TL5. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5SHZ1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEYRLKAYYR EGEKPSALRR AGKLPGVMYN RHLNRKVYVD LVEFDKVFRQ    50
    ASIHHVIVLE LPDGQSLPTL VRQVNLDKRR RRPEHVDFFV LSDEPVEMYV 100
    PLRFVGTPAG VRAGGVLQEI HRDILVKVSP RNIPEFIEVD VSGLEIGDSL 150
    HASDLKLPPG VELAVSPEET IAAVVPPEDV EKLAEEAAAE VAEPEVIKKG 200
    KEEEEE 206
    Length:206
    Mass (Da):23,205
    Last modified:December 21, 2004 - v1
    Checksum:iACC20EC1279181CD
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti43 – 453EFD → QRF AA sequence 1 PublicationCurated
    Sequence conflicti60 – 7011ELPDGQSLPTL → QLRRGTRLSPE AA sequence 1 PublicationCuratedAdd
    BLAST

    Mass spectrometryi

    Molecular mass is 23207 Da from positions 1 - 206. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008226 Genomic DNA. Translation: BAD71412.1.
    RefSeqiYP_144855.1. NC_006461.1.

    Genome annotation databases

    EnsemblBacteriaiBAD71412; BAD71412; BAD71412.
    GeneIDi3169859.
    KEGGittj:TTHA1589.
    PATRICi23958133. VBITheThe93045_1559.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008226 Genomic DNA. Translation: BAD71412.1 .
    RefSeqi YP_144855.1. 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 V 1-206 [» ]
    2HGJ X-ray 5.00 Y 1-206 [» ]
    2HGQ X-ray 5.50 Y 1-206 [» ]
    2HGU X-ray 4.51 Y 1-206 [» ]
    2J01 X-ray 2.80 Z 1-206 [» ]
    2J03 X-ray 2.80 Z 1-206 [» ]
    2V47 X-ray 3.80 Z 1-206 [» ]
    2V49 X-ray 3.80 Z 1-206 [» ]
    2WDI X-ray 3.30 Z 1-206 [» ]
    2WDJ X-ray 3.30 Z 1-206 [» ]
    2WDL X-ray 3.50 Z 1-206 [» ]
    2WDN X-ray 3.50 Z 1-206 [» ]
    2WH2 X-ray 3.45 Z 1-206 [» ]
    2WH4 X-ray 3.45 Z 1-206 [» ]
    2WRJ X-ray 3.60 Z 1-206 [» ]
    2WRL X-ray 3.60 Z 1-206 [» ]
    2WRO X-ray 3.60 Z 1-206 [» ]
    2WRR X-ray 3.60 Z 1-206 [» ]
    2X9S X-ray 3.10 Z 1-206 [» ]
    2X9U X-ray 3.10 Z 1-206 [» ]
    2XG0 X-ray 3.20 Z 1-206 [» ]
    2XG2 X-ray 3.20 Z 1-206 [» ]
    2XQE X-ray 3.10 Z 1-206 [» ]
    2XTG electron microscopy 7.80 Z 1-206 [» ]
    2XUX electron microscopy 7.60 Z 1-206 [» ]
    2Y0V X-ray 3.10 Z 1-206 [» ]
    2Y0X X-ray 3.10 Z 1-206 [» ]
    2Y0Z X-ray 3.10 Z 1-206 [» ]
    2Y11 X-ray 3.10 Z 1-206 [» ]
    2Y13 X-ray 3.10 Z 1-206 [» ]
    2Y15 X-ray 3.10 Z 1-206 [» ]
    2Y17 X-ray 3.10 Z 1-206 [» ]
    2Y19 X-ray 3.10 Z 1-206 [» ]
    3FIN electron microscopy 6.40 Z 3-179 [» ]
    3HUX X-ray 3.10 Z 1-206 [» ]
    3HUZ X-ray 3.10 Z 1-206 [» ]
    3I8F X-ray 3.10 V 1-206 [» ]
    3I8I X-ray 3.10 V 1-206 [» ]
    3I9C X-ray 3.50 V 1-206 [» ]
    3I9E X-ray 3.50 V 1-206 [» ]
    3KIR X-ray 3.30 Z 1-206 [» ]
    3KIT X-ray 3.30 Z 1-206 [» ]
    3KIW X-ray 3.60 Z 1-206 [» ]
    3KIY X-ray 3.60 Z 1-206 [» ]
    3KNI X-ray 3.00 Z 1-206 [» ]
    3KNK X-ray 3.00 Z 1-206 [» ]
    3KNM X-ray 3.45 Z 1-206 [» ]
    3KNO X-ray 3.45 Z 1-206 [» ]
    3TVE X-ray 3.10 V 1-175 [» ]
    3TVH X-ray 3.10 V 1-179 [» ]
    3UXQ X-ray 3.20 Z 1-206 [» ]
    3UXR X-ray 3.20 Z 1-206 [» ]
    3UYE X-ray 3.00 V 1-206 [» ]
    3UYG X-ray 3.00 V 1-206 [» ]
    3UZ1 X-ray 3.30 V 1-206 [» ]
    3UZ2 X-ray 3.30 V 1-206 [» ]
    3UZ8 X-ray 3.00 V 1-206 [» ]
    3UZ9 X-ray 3.00 V 1-206 [» ]
    3UZF X-ray 3.30 V 1-206 [» ]
    3UZH X-ray 3.30 V 1-206 [» ]
    3UZK X-ray 3.30 V 1-206 [» ]
    3UZN X-ray 3.30 V 1-206 [» ]
    3V23 X-ray 3.00 Z 1-206 [» ]
    3V25 X-ray 3.00 Z 1-206 [» ]
    3V27 X-ray 3.10 Z 1-206 [» ]
    3V29 X-ray 3.10 Z 1-206 [» ]
    3V2D X-ray 2.70 Z 1-206 [» ]
    3V2F X-ray 2.70 Z 1-206 [» ]
    3V6W X-ray 3.90 Z 1-206 [» ]
    3V6X X-ray 3.90 Z 1-206 [» ]
    3ZN9 X-ray 3.10 Z 1-206 [» ]
    3ZNE X-ray 3.10 Z 1-206 [» ]
    3ZVP X-ray 3.80 Z 1-206 [» ]
    4ABS X-ray 3.10 Z 1-206 [» ]
    4B8G X-ray 3.70 Z 1-206 [» ]
    4B8I X-ray 3.70 Z 1-206 [» ]
    4BTD X-ray 2.95 Z 2-206 [» ]
    4BYC X-ray 3.35 Z 1-206 [» ]
    4BYE X-ray 3.35 Z 1-206 [» ]
    4DHA X-ray 3.20 Z 1-206 [» ]
    4DHC X-ray 3.20 Z 1-206 [» ]
    4EJB X-ray 3.52 Z 1-206 [» ]
    4EJC X-ray 3.52 Z 1-206 [» ]
    4G5L X-ray 3.30 V 1-206 [» ]
    4G5N X-ray 3.30 V 1-206 [» ]
    4G5U X-ray 3.10 V 1-206 [» ]
    4G5W X-ray 3.10 V 1-206 [» ]
    4JUX X-ray 2.86 Z 1-206 [» ]
    4K0M X-ray 3.30 Z 3-178 [» ]
    4K0Q X-ray 3.30 Z 3-178 [» ]
    4NVV X-ray 3.00 Z 1-206 [» ]
    4NVX X-ray 3.00 Z 1-206 [» ]
    4NVZ X-ray 3.10 Z 1-206 [» ]
    4NW1 X-ray 3.10 Z 1-206 [» ]
    ProteinModelPortali Q5SHZ1.
    SMRi Q5SHZ1. Positions 1-185.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 300852.TTHA1589.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD71412 ; BAD71412 ; BAD71412 .
    GeneIDi 3169859.
    KEGGi ttj:TTHA1589.
    PATRICi 23958133. VBITheThe93045_1559.

    Phylogenomic databases

    eggNOGi COG1825.
    HOGENOMi HOG000214906.
    KOi K02897.
    OMAi CIGVKLG.
    OrthoDBi EOG6SZ1PC.
    PhylomeDBi Q5SHZ1.

    Enzyme and pathway databases

    BioCyci TTHE300852:GH8R-1628-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q5SHZ1.

    Family and domain databases

    Gene3Di 2.170.120.20. 1 hit.
    2.40.240.10. 1 hit.
    HAMAPi MF_01334. Ribosomal_L25_CTC.
    InterProi IPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
    IPR011035. Ribosomal_L25/Gln-tRNA_synth.
    IPR020057. Ribosomal_L25_b-dom.
    IPR001021. Ribosomal_L25_long.
    [Graphical view ]
    Pfami PF14693. Ribosomal_TL5_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50715. SSF50715. 1 hit.
    TIGRFAMsi TIGR00731. ctc_TL5. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "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.
    2. "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 1-70.
    3. "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 1-30.
    4. "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 1-22, ISOLATION OF 5S RRNA-ASSOCIATED COMPLEXES.
    5. "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.
    6. "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.
    7. Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.

    Entry informationi

    Entry nameiRL25_THET8
    AccessioniPrimary (citable) accession number: Q5SHZ1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: December 21, 2004
    Last modified: October 1, 2014
    This is version 86 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

    External Data

    Dasty 3