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Protein

Ribonuclease P protein component 4

Gene

rnp4

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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.UniRule annotation3 Publications

Catalytic activityi

Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor.UniRule annotation1 Publication

Cofactori

Zn2+UniRule annotation2 PublicationsNote: Binds 1 zinc ion per subunit.UniRule annotation2 Publications

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 – 631ZincUniRule annotation2 Publications
    Metal bindingi66 – 661ZincUniRule annotation2 Publications
    Metal bindingi92 – 921ZincUniRule annotation2 Publications
    Metal bindingi95 – 951ZincUniRule annotation2 Publications

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BRENDAi3.1.26.5. 5243.

    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 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    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 – 3116Combined sources
    Helixi33 – 5018Combined sources
    Turni57 – 604Combined sources
    Turni64 – 663Combined sources
    Turni72 – 743Combined sources
    Beta strandi75 – 817Combined sources
    Beta strandi83 – 853Combined sources
    Beta strandi87 – 926Combined sources
    Turni93 – 953Combined sources
    Beta strandi98 – 1025Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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

            10         20         30         40         50
    MAKYNEKKEK KRIAKERIDI LFSLAERVFP YSPELAKRYV ELALLVQQKA
    60 70 80 90 100
    KVKIPRKWKR RYCKKCHAFL VPGINARVRL RQKRMPHIVV KCLECGHIMR
    110
    YPYIKEIKKR RKEKMEY
    Length:117
    Mass (Da):14,303
    Last modified:June 1, 2002 - v1
    Checksum:i876CD8CC664F3F38
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE009950 Genomic DNA. Translation: AAL81737.1.
    RefSeqiNP_579342.1. NC_003413.1.
    WP_011012760.1. NC_003413.1.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE009950 Genomic DNA. Translation: AAL81737.1.
    RefSeqiNP_579342.1. NC_003413.1.
    WP_011012760.1. NC_003413.1.

    3D structure databases

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

    Protein-protein interaction databases

    STRINGi186497.PF1613.

    Proteomic databases

    PRIDEiQ8U0H6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiCOG2023.
    HOGENOMiHOG000230709.
    KOiK03540.
    OMAiPRKWKRR.

    Enzyme and pathway databases

    BRENDAi3.1.26.5. 5243.

    Miscellaneous databases

    EvolutionaryTraceiQ8U0H6.

    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.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    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: May 27, 2015
    This is version 69 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

    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.