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Q8U0H6

- RNP4_PYRFU

UniProt

Q8U0H6 - RNP4_PYRFU

Protein

Ribonuclease P protein component 4

Gene

rnp4

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 63 (01 Oct 2014)
      Sequence version 1 (01 Jun 2002)
      Previous versions | rss
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    Functioni

    Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg2+ needed for activity.3 PublicationsUniRule annotation

    Catalytic activityi

    Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor.1 PublicationUniRule annotation

    Cofactori

    Binds 1 zinc ion per subunit.2 PublicationsUniRule annotation

    Kineticsi

    kcat is 9.5 min(-1). For enzyme reconstituted with RNA and 4 known subunits (Rnp1-4).

    1. KM=0.18 µM for E.coli pre-tRNA(Tyr)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi63 – 631Zinc2 PublicationsUniRule annotation
    Metal bindingi66 – 661Zinc2 PublicationsUniRule annotation
    Metal bindingi92 – 921Zinc2 PublicationsUniRule annotation
    Metal bindingi95 – 951Zinc2 PublicationsUniRule annotation

    GO - Molecular functioni

    1. ribonuclease P activity Source: UniProtKB-HAMAP
    2. zinc ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. tRNA 5'-leader removal Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonuclease P protein component 4UniRule annotation (EC:3.1.26.5UniRule annotation)
    Short name:
    RNase P component 4UniRule annotation
    Alternative name(s):
    Rpp21UniRule annotation
    Gene namesi
    Name:rnp4UniRule annotation
    Ordered Locus Names:PF1613
    OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
    Taxonomic identifieri186497 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000001013: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. ribonuclease P complex Source: UniProtKB-HAMAP

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi14 – 141A → V: 3-fold reduced binding to Rnp1. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 117117Ribonuclease P protein component 4PRO_0000153859Add
    BLAST

    Proteomic databases

    PRIDEiQ8U0H6.

    Interactioni

    Subunit structurei

    Consists of a catalytic RNA component and at least 4 protein subunits. Forms a subcomplex with Rnp1 which stimulates the catalytic RNA.5 Publications

    Protein-protein interaction databases

    STRINGi186497.PF1613.

    Structurei

    Secondary structure

    1
    117
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi16 – 3116
    Helixi33 – 5018
    Turni57 – 604
    Turni64 – 663
    Turni72 – 743
    Beta strandi75 – 817
    Beta strandi83 – 853
    Beta strandi87 – 926
    Turni93 – 953
    Beta strandi98 – 1025

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2K3RNMR-A1-117[»]
    2KI7NMR-B1-117[»]
    ProteinModelPortaliQ8U0H6.
    SMRiQ8U0H6. Positions 13-104.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8U0H6.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the eukaryotic/archaeal RNase P protein component 4 family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG2023.
    HOGENOMiHOG000230709.
    KOiK03540.
    OMAiPRKWKRR.

    Family and domain databases

    HAMAPiMF_00757. RNase_P_4.
    InterProiIPR016432. RNase_P_comp-4.
    IPR007175. Rpr2.
    [Graphical view]
    PANTHERiPTHR14742. PTHR14742. 1 hit.
    PfamiPF04032. Rpr2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004878. RNase_P_4. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q8U0H6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAKYNEKKEK KRIAKERIDI LFSLAERVFP YSPELAKRYV ELALLVQQKA    50
    KVKIPRKWKR RYCKKCHAFL VPGINARVRL RQKRMPHIVV KCLECGHIMR 100
    YPYIKEIKKR RKEKMEY 117
    Length:117
    Mass (Da):14,303
    Last modified:June 1, 2002 - v1
    Checksum:i876CD8CC664F3F38
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009950 Genomic DNA. Translation: AAL81737.1.
    RefSeqiNP_579342.1. NC_003413.1.

    Genome annotation databases

    EnsemblBacteriaiAAL81737; AAL81737; PF1613.
    GeneIDi1469490.
    KEGGipfu:PF1613.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009950 Genomic DNA. Translation: AAL81737.1 .
    RefSeqi NP_579342.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2K3R NMR - A 1-117 [» ]
    2KI7 NMR - B 1-117 [» ]
    ProteinModelPortali Q8U0H6.
    SMRi Q8U0H6. Positions 13-104.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 186497.PF1613.

    Proteomic databases

    PRIDEi Q8U0H6.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL81737 ; AAL81737 ; PF1613 .
    GeneIDi 1469490.
    KEGGi pfu:PF1613.

    Phylogenomic databases

    eggNOGi COG2023.
    HOGENOMi HOG000230709.
    KOi K03540.
    OMAi PRKWKRR.

    Miscellaneous databases

    EvolutionaryTracei Q8U0H6.

    Family and domain databases

    HAMAPi MF_00757. RNase_P_4.
    InterProi IPR016432. RNase_P_comp-4.
    IPR007175. Rpr2.
    [Graphical view ]
    PANTHERi PTHR14742. PTHR14742. 1 hit.
    Pfami PF04032. Rpr2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF004878. RNase_P_4. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
      Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
      Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    2. "Functional reconstitution and characterization of Pyrococcus furiosus RNase P."
      Tsai H.Y., Pulukkunat D.K., Woznick W.K., Gopalan V.
      Proc. Natl. Acad. Sci. U.S.A. 103:16147-16152(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    3. "Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P."
      Chen W.Y., Xu Y., Cho I.M., Oruganti S.V., Foster M.P., Gopalan V.
      J. Mol. Biol. 411:368-383(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH RNP1, SUBUNIT.
    4. "Fidelity of tRNA 5'-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors."
      Chen W.Y., Singh D., Lai L.B., Stiffler M.A., Lai H.D., Foster M.P., Gopalan V.
      Nucleic Acids Res. 40:4666-4680(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH RNP1, SUBUNIT.
    5. "Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner."
      Amero C.D., Boomershine W.P., Xu Y., Foster M.
      Biochemistry 47:11704-11710(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR IN COMPLEX WITH ZINC, INTERACTION WITH RNP1, SUBUNIT, COFACTOR.
    6. "Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions."
      Xu Y., Amero C.D., Pulukkunat D.K., Gopalan V., Foster M.P.
      J. Mol. Biol. 393:1043-1055(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR IN COMPLEX WITH RNP1 AND ZINC, COFACTOR, SUBUNIT, MUTAGENESIS OF ALA-14.

    Entry informationi

    Entry nameiRNP4_PYRFU
    AccessioniPrimary (citable) accession number: Q8U0H6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 5, 2004
    Last sequence update: June 1, 2002
    Last modified: October 1, 2014
    This is version 63 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, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3