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O59248 (RNP4_PYRHO) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 76. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonuclease P protein component 4

Short name=RNase P component 4
EC=3.1.26.5
Alternative name(s):
Rpp21
Gene names
Name:rnp4
Ordered Locus Names:PH1601
OrganismPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]
Taxonomic identifier70601 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Protein attributes

Sequence length120 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Binds RNase P RNA. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6

Catalytic activity

Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. HAMAP-Rule MF_00757

Cofactor

Binds 1 zinc ion per subunit. Ref.5 Ref.6

Subunit structure

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. Ref.2 Ref.3 Ref.4 Ref.6

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00757.

Sequence similarities

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

Biophysicochemical properties

Temperature dependence:

Optimum temperature is 70 degrees Celsius. Ref.2 Ref.3

Binary interactions

With

Entry

#Exp.

IntAct

Notes

rnp2O591503EBI-2641275,EBI-2603177

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 120120Ribonuclease P protein component 4 HAMAP-Rule MF_00757
PRO_0000153860

Sites

Metal binding681Zinc
Metal binding711Zinc
Metal binding971Zinc
Metal binding1001Zinc

Experimental info

Mutagenesis221R → A: 40% reconstituted RNase P activity. Ref.5
Mutagenesis441Y → A: 40% reconstituted RNase P activity. Ref.5
Mutagenesis651R → A: 70% reconstituted RNase P activity. Ref.5
Mutagenesis68 – 714CKRC → SKRS: Does not reconstitute RNase P activity. Protein destabilized. Ref.5
Mutagenesis691K → A: 10% reconstituted RNase P activity. Ref.5
Mutagenesis841R → A: 50% reconstituted RNase P activity. Ref.5
Mutagenesis861R → A: 20% reconstituted RNase P activity. Ref.5
Mutagenesis97 – 1004CLEC → SLES: Does not reconstitute RNase P activity. Protein destabilized. Ref.5
Mutagenesis1051R → A: Does not reconstitute RNase P activity. Ref.5

Secondary structure

................... 120
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O59248 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: 2AC453B35C964AE6

FASTA12014,589
        10         20         30         40         50         60 
MVDIVKRRDW EKKEKKKIAI ERIDTLFTLA ERVARYSPDL AKRYVELALE IQKKAKVKIP 

        70         80         90        100        110        120 
RKWKRRYCKR CHTFLIPGVN ARVRLRTKRM PHVVITCLEC GYIMRYPYLR EVKQKRKKAT 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3."
Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. expand/collapse author list , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.
DNA Res. 5:55-76(1998) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BA000001 Genomic DNA. Translation: BAA30713.1.
PIRA71039.
RefSeqNP_143456.1. NC_000961.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1X0TX-ray1.60A1-120[»]
2ZAEX-ray2.21B/D1-120[»]
ProteinModelPortalO59248.
SMRO59248. Positions 4-109.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActO59248. 2 interactions.
STRING70601.PH1601.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAA30713; BAA30713; BAA30713.
GeneID1442455.
KEGGpho:PH1601.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG2023.
HOGENOMHOG000230709.
KOK03540.
OMAPRKWKRR.

Enzyme and pathway databases

BioCycPHOR70601:GJWR-1604-MONOMER.

Family and domain databases

HAMAPMF_00757. RNase_P_4.
InterProIPR016432. RNase_P_comp-4.
IPR007175. Rpr2.
[Graphical view]
PANTHERPTHR14742. PTHR14742. 1 hit.
PfamPF04032. Rpr2. 1 hit.
[Graphical view]
PIRSFPIRSF004878. RNase_P_4. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO59248.

Entry information

Entry nameRNP4_PYRHO
AccessionPrimary (citable) accession number: O59248
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: August 1, 1998
Last modified: July 9, 2014
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references