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Q8U0H6 (RNP4_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 62. 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·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:PF1613
OrganismPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]
Taxonomic identifier186497 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Protein attributes

Sequence length117 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. 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. Ref.2 Ref.3 Ref.4

Catalytic activity

Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Ref.2

Cofactor

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

Subunit structure

Consists of a catalytic RNA component and at least 4 protein subunits. Forms a subcomplex with Rnp1 which stimulates the catalytic RNA. Ref.2 Ref.3 Ref.4 Ref.5 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

Kinetic parameters:

kcat is 9.5 min(-1). For enzyme reconstituted with RNA and 4 known subunits (Rnp1-4).

KM=0.18 µM for E.coli pre-tRNA(Tyr) Ref.2

Ontologies

Keywords
   Biological processtRNA processing
   Cellular componentCytoplasm
   LigandMetal-binding
Zinc
   Molecular functionEndonuclease
Hydrolase
Nuclease
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processtRNA 5'-leader removal

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

ribonuclease P complex

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Molecular_functionribonuclease P activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

zinc ion binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 117117Ribonuclease P protein component 4 HAMAP-Rule MF_00757
PRO_0000153859

Sites

Metal binding631Zinc
Metal binding661Zinc
Metal binding921Zinc
Metal binding951Zinc

Experimental info

Mutagenesis141A → V: 3-fold reduced binding to Rnp1. Ref.6

Secondary structure

................... 117
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q8U0H6 [UniParc].

Last modified June 1, 2002. Version 1.
Checksum: 876CD8CC664F3F38

FASTA11714,303
        10         20         30         40         50         60 
MAKYNEKKEK KRIAKERIDI LFSLAERVFP YSPELAKRYV ELALLVQQKA KVKIPRKWKR 

        70         80         90        100        110 
RYCKKCHAFL VPGINARVRL RQKRMPHIVV KCLECGHIMR YPYIKEIKKR RKEKMEY 

« Hide

References

« Hide 'large scale' references
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE009950 Genomic DNA. Translation: AAL81737.1.
RefSeqNP_579342.1. NC_003413.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2K3RNMR-A1-117[»]
2KI7NMR-B1-117[»]
ProteinModelPortalQ8U0H6.
SMRQ8U0H6. Positions 13-104.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING186497.PF1613.

Proteomic databases

PRIDEQ8U0H6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL81737; AAL81737; PF1613.
GeneID1469490.
KEGGpfu:PF1613.

Phylogenomic databases

eggNOGCOG2023.
HOGENOMHOG000230709.
KOK03540.
OMAPRKWKRR.

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

EvolutionaryTraceQ8U0H6.

Entry information

Entry nameRNP4_PYRFU
AccessionPrimary (citable) accession number: Q8U0H6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: June 1, 2002
Last modified: July 9, 2014
This is version 62 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