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O59248

- RNP4_PYRHO

UniProt

O59248 - RNP4_PYRHO

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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

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

Zn2+2 PublicationsUniRule annotationNote: 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. ribonuclease P activity Source: UniProtKB
  2. 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
Complete GO annotation...

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-HAMAP
  2. ribonuclease P complex Source: UniProtKB
Complete GO annotation...

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. 1 Publication
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. 1 Publication
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 – 3430Combined sources
Helixi38 – 5518Combined sources
Turni61 – 655Combined sources
Turni69 – 713Combined sources
Turni77 – 793Combined sources
Beta strandi80 – 867Combined sources
Beta strandi88 – 903Combined sources
Beta strandi92 – 976Combined sources
Turni98 – 1003Combined sources
Beta strandi103 – 1075Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MVDIVKRRDW EKKEKKKIAI ERIDTLFTLA ERVARYSPDL AKRYVELALE
60 70 80 90 100
IQKKAKVKIP RKWKRRYCKR CHTFLIPGVN ARVRLRTKRM PHVVITCLEC
110 120
GYIMRYPYLR EVKQKRKKAT
Length:120
Mass (Da):14,589
Last modified:August 1, 1998 - v1
Checksum:i2AC453B35C964AE6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30713.1.
PIRiA71039.
RefSeqiNP_143456.1. NC_000961.1.
WP_010885676.1. NC_000961.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30713.1 .
PIRi A71039.
RefSeqi NP_143456.1. NC_000961.1.
WP_010885676.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 79 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