Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q5SHN9

- RL4_THET8

UniProt

Q5SHN9 - RL4_THET8

Protein

50S ribosomal protein L4

Gene

rplD

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome By similarity.By similarity
    Forms part of the polypeptide exit tunnel.By similarity
    This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome.

    GO - Molecular functioni

    1. rRNA binding Source: UniProtKB-HAMAP
    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-1730-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    50S ribosomal protein L4
    Alternative name(s):
    L1e
    Gene namesi
    Name:rplD
    Ordered Locus Names:TTHA1691
    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

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi55 – 551G → A: Increases Ptase activity of hybrid ribosomes to a value greater than that of pure E.coli ribosomes. Increases binding of a tRNA analog to the P site. 1 Publication
    Mutagenesisi55 – 551G → S: No effect on Ptase activity of hybrid ribosomes. No change in binding of a tRNA analog to the A or P site. 1 Publication
    Mutagenesisi56 – 561E → A: Further decreases Ptase activity in E.coli hybrid ribosomes. Significantly decreases binding of a tRNA analog to the A or P site. 1 Publication
    Mutagenesisi56 – 561E → Q: Restores Ptase activity of hybrid ribosomes to that of pure E.coli ribosomes. Significantly increases binding of a tRNA analog to the P site. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 21021050S ribosomal protein L4PRO_0000129300Add
    BLAST

    Post-translational modificationi

    The N-terminus is blocked.

    Interactioni

    Subunit structurei

    Part of the 50S ribosomal subunit.

    Protein-protein interaction databases

    STRINGi300852.TTHA1691.

    Structurei

    Secondary structure

    1
    210
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 103
    Beta strandi11 – 133
    Beta strandi14 – 163
    Helixi21 – 233
    Beta strandi24 – 263
    Helixi30 – 4314
    Turni54 – 563
    Beta strandi57 – 593
    Beta strandi67 – 726
    Beta strandi78 – 803
    Beta strandi83 – 864
    Beta strandi88 – 903
    Helixi103 – 11917
    Beta strandi123 – 1275
    Helixi136 – 14510
    Beta strandi150 – 1523
    Beta strandi154 – 1574
    Helixi161 – 1677
    Beta strandi173 – 1764
    Helixi178 – 1803
    Helixi183 – 1886
    Beta strandi189 – 1957
    Helixi196 – 20611

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GIYX-ray5.50F1-210[»]
    1TWVmodel-D1-210[»]
    1YL3X-ray5.50F1-210[»]
    2HGJX-ray5.00F1-210[»]
    2HGQX-ray5.50F1-210[»]
    2HGUX-ray4.51F1-210[»]
    2J01X-ray2.80F1-210[»]
    2J03X-ray2.80F1-210[»]
    2V47X-ray3.80F1-210[»]
    2V49X-ray3.80F1-210[»]
    2WDIX-ray3.30F1-210[»]
    2WDJX-ray3.30F1-210[»]
    2WDLX-ray3.50F1-210[»]
    2WDNX-ray3.50F1-210[»]
    2WH2X-ray3.45F1-210[»]
    2WH4X-ray3.45F1-210[»]
    2WRJX-ray3.60F1-210[»]
    2WRLX-ray3.60F1-210[»]
    2WROX-ray3.60F1-210[»]
    2WRRX-ray3.60F1-210[»]
    2X9SX-ray3.10F1-210[»]
    2X9UX-ray3.10F1-210[»]
    2XG0X-ray3.20F1-210[»]
    2XG2X-ray3.20F1-210[»]
    2XQEX-ray3.10F1-210[»]
    2XTGelectron microscopy7.80F1-210[»]
    2XUXelectron microscopy7.60F1-210[»]
    2Y0VX-ray3.10F1-210[»]
    2Y0XX-ray3.10F1-210[»]
    2Y0ZX-ray3.10F1-210[»]
    2Y11X-ray3.10F1-210[»]
    2Y13X-ray3.10F1-210[»]
    2Y15X-ray3.10F1-210[»]
    2Y17X-ray3.10F1-210[»]
    2Y19X-ray3.10F1-210[»]
    3F1FX-ray3.00F1-210[»]
    3F1HX-ray3.00F1-210[»]
    3FINelectron microscopy6.40F1-208[»]
    3HUXX-ray3.10F1-210[»]
    3HUZX-ray3.10F1-210[»]
    3I8FX-ray3.10F1-210[»]
    3I8IX-ray3.10F1-210[»]
    3I9CX-ray3.50F1-210[»]
    3I9EX-ray3.50F1-210[»]
    3KIRX-ray3.30F1-210[»]
    3KITX-ray3.30F1-210[»]
    3KIWX-ray3.60F1-210[»]
    3KIYX-ray3.60F1-210[»]
    3KNIX-ray3.00F1-210[»]
    3KNKX-ray3.00F1-210[»]
    3KNMX-ray3.45F1-210[»]
    3KNOX-ray3.45F1-210[»]
    3OHJX-ray3.00F1-210[»]
    3OHZX-ray3.00F1-210[»]
    3OI5X-ray3.10F1-210[»]
    3TVEX-ray3.10F6-207[»]
    3TVHX-ray3.10F1-208[»]
    3UXQX-ray3.20F6-210[»]
    3UXRX-ray3.20F6-210[»]
    3UYEX-ray3.00F1-210[»]
    3UYGX-ray3.00F1-210[»]
    3UZ1X-ray3.30F1-210[»]
    3UZ2X-ray3.30F1-210[»]
    3UZ8X-ray3.00F1-210[»]
    3UZ9X-ray3.00F1-210[»]
    3UZFX-ray3.30F1-210[»]
    3UZHX-ray3.30F1-210[»]
    3UZKX-ray3.30F1-210[»]
    3UZNX-ray3.30F1-210[»]
    3V23X-ray3.00F1-210[»]
    3V25X-ray3.00F1-210[»]
    3V27X-ray3.10F1-210[»]
    3V29X-ray3.10F1-210[»]
    3V2DX-ray2.70F1-210[»]
    3V2FX-ray2.70F1-210[»]
    3V6WX-ray3.90F1-210[»]
    3V6XX-ray3.90F1-210[»]
    3ZN9X-ray3.10F1-210[»]
    3ZNEX-ray3.10F1-210[»]
    3ZVPX-ray3.80F1-210[»]
    4ABSX-ray3.10F1-210[»]
    4B8GX-ray3.70F1-210[»]
    4B8IX-ray3.70F1-210[»]
    4BTDX-ray2.95F1-210[»]
    4BYCX-ray3.35F1-210[»]
    4BYEX-ray3.35F1-210[»]
    4DHAX-ray3.20F1-210[»]
    4DHCX-ray3.20F1-210[»]
    4EJBX-ray3.52F1-210[»]
    4EJCX-ray3.52F1-210[»]
    4G5LX-ray3.30F1-210[»]
    4G5NX-ray3.30F1-210[»]
    4G5UX-ray3.10F1-210[»]
    4G5WX-ray3.10F1-210[»]
    4JUXX-ray2.86F1-210[»]
    4K0MX-ray3.30F1-207[»]
    4K0QX-ray3.30F1-207[»]
    4NVVX-ray3.00F1-210[»]
    4NVXX-ray3.00F1-210[»]
    4NVZX-ray3.10F1-210[»]
    4NW1X-ray3.10F1-210[»]
    ProteinModelPortaliQ5SHN9.
    SMRiQ5SHN9. Positions 3-210.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SHN9.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein L4P family.Curated

    Phylogenomic databases

    eggNOGiCOG0088.
    HOGENOMiHOG000248767.
    KOiK02926.
    OMAiRSIMANQ.
    OrthoDBiEOG6M0T9G.

    Family and domain databases

    Gene3Di3.40.1370.10. 1 hit.
    HAMAPiMF_01328_B. Ribosomal_L4_B.
    InterProiIPR002136. Ribosomal_L4/L1e.
    IPR013005. Ribosomal_L4/L1e_bac-type.
    IPR023574. Ribosomal_L4_dom.
    [Graphical view]
    PANTHERiPTHR10746. PTHR10746. 1 hit.
    PfamiPF00573. Ribosomal_L4. 1 hit.
    [Graphical view]
    SUPFAMiSSF52166. SSF52166. 1 hit.
    TIGRFAMsiTIGR03953. rplD_bact. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5SHN9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKEVAVYQIP VLSPSGRREL AADLPAEINP HLLWEVVRWQ LAKRRRGTAS    50
    TKTRGEVAYS GRKIWPQKHT GRARHGDIGA PIFVGGGVVF GPKPRDYSYT 100
    LPKKVRKKGL AMAVADRARE GKLLLVEAFA GVNGKTKEFL AWAKEAGLDG 150
    SESVLLVTGN ELVRRAARNL PWVVTLAPEG LNVYDIVRTE RLVMDLDAWE 200
    VFQNRIGGEA 210
    Length:210
    Mass (Da):23,235
    Last modified:December 21, 2004 - v1
    Checksum:iBFB99AC179C110B4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti19 – 202EL → DV in AAA97862. (PubMed:8566766)Curated

    Mass spectrometryi

    Molecular mass is 22724 Da from positions 1 - 210. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U36480 Genomic DNA. Translation: AAA97862.1.
    AP008226 Genomic DNA. Translation: BAD71514.1.
    RefSeqiYP_144957.2. NC_006461.1.

    Genome annotation databases

    EnsemblBacteriaiBAD71514; BAD71514; BAD71514.
    GeneIDi3167923.
    KEGGittj:TTHA1691.
    PATRICi23958337. VBITheThe93045_1661.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U36480 Genomic DNA. Translation: AAA97862.1 .
    AP008226 Genomic DNA. Translation: BAD71514.1 .
    RefSeqi YP_144957.2. 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 F 1-210 [» ]
    1TWV model - D 1-210 [» ]
    1YL3 X-ray 5.50 F 1-210 [» ]
    2HGJ X-ray 5.00 F 1-210 [» ]
    2HGQ X-ray 5.50 F 1-210 [» ]
    2HGU X-ray 4.51 F 1-210 [» ]
    2J01 X-ray 2.80 F 1-210 [» ]
    2J03 X-ray 2.80 F 1-210 [» ]
    2V47 X-ray 3.80 F 1-210 [» ]
    2V49 X-ray 3.80 F 1-210 [» ]
    2WDI X-ray 3.30 F 1-210 [» ]
    2WDJ X-ray 3.30 F 1-210 [» ]
    2WDL X-ray 3.50 F 1-210 [» ]
    2WDN X-ray 3.50 F 1-210 [» ]
    2WH2 X-ray 3.45 F 1-210 [» ]
    2WH4 X-ray 3.45 F 1-210 [» ]
    2WRJ X-ray 3.60 F 1-210 [» ]
    2WRL X-ray 3.60 F 1-210 [» ]
    2WRO X-ray 3.60 F 1-210 [» ]
    2WRR X-ray 3.60 F 1-210 [» ]
    2X9S X-ray 3.10 F 1-210 [» ]
    2X9U X-ray 3.10 F 1-210 [» ]
    2XG0 X-ray 3.20 F 1-210 [» ]
    2XG2 X-ray 3.20 F 1-210 [» ]
    2XQE X-ray 3.10 F 1-210 [» ]
    2XTG electron microscopy 7.80 F 1-210 [» ]
    2XUX electron microscopy 7.60 F 1-210 [» ]
    2Y0V X-ray 3.10 F 1-210 [» ]
    2Y0X X-ray 3.10 F 1-210 [» ]
    2Y0Z X-ray 3.10 F 1-210 [» ]
    2Y11 X-ray 3.10 F 1-210 [» ]
    2Y13 X-ray 3.10 F 1-210 [» ]
    2Y15 X-ray 3.10 F 1-210 [» ]
    2Y17 X-ray 3.10 F 1-210 [» ]
    2Y19 X-ray 3.10 F 1-210 [» ]
    3F1F X-ray 3.00 F 1-210 [» ]
    3F1H X-ray 3.00 F 1-210 [» ]
    3FIN electron microscopy 6.40 F 1-208 [» ]
    3HUX X-ray 3.10 F 1-210 [» ]
    3HUZ X-ray 3.10 F 1-210 [» ]
    3I8F X-ray 3.10 F 1-210 [» ]
    3I8I X-ray 3.10 F 1-210 [» ]
    3I9C X-ray 3.50 F 1-210 [» ]
    3I9E X-ray 3.50 F 1-210 [» ]
    3KIR X-ray 3.30 F 1-210 [» ]
    3KIT X-ray 3.30 F 1-210 [» ]
    3KIW X-ray 3.60 F 1-210 [» ]
    3KIY X-ray 3.60 F 1-210 [» ]
    3KNI X-ray 3.00 F 1-210 [» ]
    3KNK X-ray 3.00 F 1-210 [» ]
    3KNM X-ray 3.45 F 1-210 [» ]
    3KNO X-ray 3.45 F 1-210 [» ]
    3OHJ X-ray 3.00 F 1-210 [» ]
    3OHZ X-ray 3.00 F 1-210 [» ]
    3OI5 X-ray 3.10 F 1-210 [» ]
    3TVE X-ray 3.10 F 6-207 [» ]
    3TVH X-ray 3.10 F 1-208 [» ]
    3UXQ X-ray 3.20 F 6-210 [» ]
    3UXR X-ray 3.20 F 6-210 [» ]
    3UYE X-ray 3.00 F 1-210 [» ]
    3UYG X-ray 3.00 F 1-210 [» ]
    3UZ1 X-ray 3.30 F 1-210 [» ]
    3UZ2 X-ray 3.30 F 1-210 [» ]
    3UZ8 X-ray 3.00 F 1-210 [» ]
    3UZ9 X-ray 3.00 F 1-210 [» ]
    3UZF X-ray 3.30 F 1-210 [» ]
    3UZH X-ray 3.30 F 1-210 [» ]
    3UZK X-ray 3.30 F 1-210 [» ]
    3UZN X-ray 3.30 F 1-210 [» ]
    3V23 X-ray 3.00 F 1-210 [» ]
    3V25 X-ray 3.00 F 1-210 [» ]
    3V27 X-ray 3.10 F 1-210 [» ]
    3V29 X-ray 3.10 F 1-210 [» ]
    3V2D X-ray 2.70 F 1-210 [» ]
    3V2F X-ray 2.70 F 1-210 [» ]
    3V6W X-ray 3.90 F 1-210 [» ]
    3V6X X-ray 3.90 F 1-210 [» ]
    3ZN9 X-ray 3.10 F 1-210 [» ]
    3ZNE X-ray 3.10 F 1-210 [» ]
    3ZVP X-ray 3.80 F 1-210 [» ]
    4ABS X-ray 3.10 F 1-210 [» ]
    4B8G X-ray 3.70 F 1-210 [» ]
    4B8I X-ray 3.70 F 1-210 [» ]
    4BTD X-ray 2.95 F 1-210 [» ]
    4BYC X-ray 3.35 F 1-210 [» ]
    4BYE X-ray 3.35 F 1-210 [» ]
    4DHA X-ray 3.20 F 1-210 [» ]
    4DHC X-ray 3.20 F 1-210 [» ]
    4EJB X-ray 3.52 F 1-210 [» ]
    4EJC X-ray 3.52 F 1-210 [» ]
    4G5L X-ray 3.30 F 1-210 [» ]
    4G5N X-ray 3.30 F 1-210 [» ]
    4G5U X-ray 3.10 F 1-210 [» ]
    4G5W X-ray 3.10 F 1-210 [» ]
    4JUX X-ray 2.86 F 1-210 [» ]
    4K0M X-ray 3.30 F 1-207 [» ]
    4K0Q X-ray 3.30 F 1-207 [» ]
    4NVV X-ray 3.00 F 1-210 [» ]
    4NVX X-ray 3.00 F 1-210 [» ]
    4NVZ X-ray 3.10 F 1-210 [» ]
    4NW1 X-ray 3.10 F 1-210 [» ]
    ProteinModelPortali Q5SHN9.
    SMRi Q5SHN9. Positions 3-210.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 300852.TTHA1691.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD71514 ; BAD71514 ; BAD71514 .
    GeneIDi 3167923.
    KEGGi ttj:TTHA1691.
    PATRICi 23958337. VBITheThe93045_1661.

    Phylogenomic databases

    eggNOGi COG0088.
    HOGENOMi HOG000248767.
    KOi K02926.
    OMAi RSIMANQ.
    OrthoDBi EOG6M0T9G.

    Enzyme and pathway databases

    BioCyci TTHE300852:GH8R-1730-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q5SHN9.

    Family and domain databases

    Gene3Di 3.40.1370.10. 1 hit.
    HAMAPi MF_01328_B. Ribosomal_L4_B.
    InterProi IPR002136. Ribosomal_L4/L1e.
    IPR013005. Ribosomal_L4/L1e_bac-type.
    IPR023574. Ribosomal_L4_dom.
    [Graphical view ]
    PANTHERi PTHR10746. PTHR10746. 1 hit.
    Pfami PF00573. Ribosomal_L4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52166. SSF52166. 1 hit.
    TIGRFAMsi TIGR03953. rplD_bact. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Direct linkage of str-, S10- and spc-related gene clusters in Thermus thermophilus HB8, and sequences of ribosomal proteins L4 and S10."
      Pfeiffer T., Jorcke D., Feltens R., Hartmann R.K.
      Gene 167:141-145(1995) [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 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 6-17, BLOCKAGE OF N-TERMINUS.
    4. "On the structural and functional importance of the highly conserved Glu56 of Thermus thermophilus L4 ribosomal protein."
      Leontiadou F., Xaplanteri M.A., Papadopoulos G., Gerassimou C., Kalpaxis D.L., Choli-Papadopoulou T.
      J. Mol. Biol. 332:73-84(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLY-55 AND GLU-56.
    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 nameiRL4_THET8
    AccessioniPrimary (citable) accession number: Q5SHN9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: December 21, 2004
    Last modified: October 1, 2014
    This is version 89 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