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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
    Proteomesi
    • UP000001013 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

    eggNOGiarCOG04345. Archaea.
    COG2023. LUCA.
    HOGENOMiHOG000230709.
    KOiK03540.
    OMAiECGHIMR.

    Family and domain databases

    HAMAPiMF_00757. RNase_P_4. 1 hit.
    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.
    RefSeqiWP_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.
    RefSeqiWP_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

    eggNOGiarCOG04345. Archaea.
    COG2023. LUCA.
    HOGENOMiHOG000230709.
    KOiK03540.
    OMAiECGHIMR.

    Enzyme and pathway databases

    BRENDAi3.1.26.5. 5243.

    Miscellaneous databases

    EvolutionaryTraceiQ8U0H6.

    Family and domain databases

    HAMAPiMF_00757. RNase_P_4. 1 hit.
    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...

    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: November 11, 2015
    This is version 72 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

    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 one 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.