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O59248

- RNP4_PYRHO

UniProt

O59248 - RNP4_PYRHO

Protein

Ribonuclease P protein component 4

Gene

rnp4

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 77 (01 Oct 2014)
      Sequence version 1 (01 Aug 1998)
      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. Binds RNase P RNA.5 PublicationsUniRule annotation

    Catalytic activityi

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

    Cofactori

    Binds 1 zinc ion per subunit.2 PublicationsUniRule annotation

    Temperature dependencei

    Optimum temperature is 70 degrees Celsius.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi68 – 681Zinc
    Metal bindingi71 – 711Zinc
    Metal bindingi97 – 971Zinc
    Metal bindingi100 – 1001Zinc

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. ribonuclease P activity Source: UniProtKB
    3. zinc ion binding Source: UniProtKB

    GO - Biological processi

    1. RNA phosphodiester bond hydrolysis Source: GOC
    2. RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
    3. tRNA 5'-leader removal Source: UniProtKB

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciPHOR70601:GJWR-1604-MONOMER.

    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:PH1601
    OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
    Taxonomic identifieri70601 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000000752: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi22 – 221R → A: 40% reconstituted RNase P activity. 1 Publication
    Mutagenesisi44 – 441Y → A: 40% reconstituted RNase P activity. 1 Publication
    Mutagenesisi65 – 651R → A: 70% reconstituted RNase P activity. 1 Publication
    Mutagenesisi68 – 714CKRC → SKRS: Does not reconstitute RNase P activity. Protein destabilized.
    Mutagenesisi69 – 691K → A: 10% reconstituted RNase P activity. 1 Publication
    Mutagenesisi84 – 841R → A: 50% reconstituted RNase P activity. 1 Publication
    Mutagenesisi86 – 861R → A: 20% reconstituted RNase P activity. 1 Publication
    Mutagenesisi97 – 1004CLEC → SLES: Does not reconstitute RNase P activity. Protein destabilized.
    Mutagenesisi105 – 1051R → A: Does not reconstitute RNase P activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 120120Ribonuclease P protein component 4PRO_0000153860Add
    BLAST

    Interactioni

    Subunit structurei

    Consists of a catalytic RNA component and at least 5 protein subunits. Forms a heterodimeric subcomplex with Rnp1. Reconstituted enzyme missing individual protein subunits is suboptimally active, showing each subunit contributes to optimization of activity.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rnp2O591503EBI-2641275,EBI-2603177

    Protein-protein interaction databases

    IntActiO59248. 2 interactions.
    STRINGi70601.PH1601.

    Structurei

    Secondary structure

    1
    120
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 3430
    Helixi38 – 5518
    Turni61 – 655
    Turni69 – 713
    Turni77 – 793
    Beta strandi80 – 867
    Beta strandi88 – 903
    Beta strandi92 – 976
    Turni98 – 1003
    Beta strandi103 – 1075

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1X0TX-ray1.60A1-120[»]
    2ZAEX-ray2.21B/D1-120[»]
    ProteinModelPortaliO59248.
    SMRiO59248. Positions 4-109.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO59248.

    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.

    O59248-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVDIVKRRDW EKKEKKKIAI ERIDTLFTLA ERVARYSPDL AKRYVELALE    50
    IQKKAKVKIP RKWKRRYCKR CHTFLIPGVN ARVRLRTKRM PHVVITCLEC 100
    GYIMRYPYLR EVKQKRKKAT 120
    Length:120
    Mass (Da):14,589
    Last modified:August 1, 1998 - v1
    Checksum:i2AC453B35C964AE6
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000001 Genomic DNA. Translation: BAA30713.1.
    PIRiA71039.
    RefSeqiNP_143456.1. NC_000961.1.

    Genome annotation databases

    EnsemblBacteriaiBAA30713; BAA30713; BAA30713.
    GeneIDi1442455.
    KEGGipho:PH1601.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000001 Genomic DNA. Translation: BAA30713.1 .
    PIRi A71039.
    RefSeqi NP_143456.1. NC_000961.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1X0T X-ray 1.60 A 1-120 [» ]
    2ZAE X-ray 2.21 B/D 1-120 [» ]
    ProteinModelPortali O59248.
    SMRi O59248. Positions 4-109.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi O59248. 2 interactions.
    STRINGi 70601.PH1601.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA30713 ; BAA30713 ; BAA30713 .
    GeneIDi 1442455.
    KEGGi pho:PH1601.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci PHOR70601:GJWR-1604-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O59248.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    2. "Reconstitution of archaeal ribonuclease P from RNA and four protein components."
      Kouzuma Y., Mizoguchi M., Takagi H., Fukuhara H., Tsukamoto M., Numata T., Kimura M.
      Biochem. Biophys. Res. Commun. 306:666-673(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, RNA-BINDING.
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    3. "A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3."
      Fukuhara H., Kifusa M., Watanabe M., Terada A., Honda T., Numata T., Kakuta Y., Kimura M.
      Biochem. Biophys. Res. Commun. 343:956-964(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    4. "Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3."
      Terada A., Honda T., Fukuhara H., Hada K., Kimura M.
      J. Biochem. 140:293-298(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    5. "Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21."
      Kakuta Y., Ishimatsu I., Numata T., Kimura K., Yao M., Tanaka I., Kimura M.
      Biochemistry 44:12086-12093(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH ZN(2+), FUNCTION, COFACTOR, MUTAGENESIS OF ARG-22; TYR-44; ARG-65; 68-CYS--CYS-71; LYS-69; ARG-84; ARG-86; 97-CYS--CYS-100 AND ARG-105.
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    6. "Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P."
      Honda T., Kakuta Y., Kimura K., Saho J., Kimura M.
      J. Mol. Biol. 384:652-662(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) IN COMPLEX WITH RNP1 AND ZN(2+), FUNCTION, COFACTOR, SUBUNIT.
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

    Entry informationi

    Entry nameiRNP4_PYRHO
    AccessioniPrimary (citable) accession number: O59248
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 5, 2004
    Last sequence update: August 1, 1998
    Last modified: October 1, 2014
    This is version 77 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

    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