Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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

  1. ribonuclease P activity Source: UniProtKB-HAMAP
  2. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. tRNA 5'-leader removal Source: UniProtKB-HAMAP
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
ProteomesiUP000001013 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

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.

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:May 31, 2002 - v1
Checksum:i876CD8CC664F3F38
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81737.1.
RefSeqiNP_579342.1. 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.
RefSeqiNP_579342.1. 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

eggNOGiCOG2023.
HOGENOMiHOG000230709.
KOiK03540.
OMAiPRKWKRR.

Enzyme and pathway databases

BRENDAi3.1.26.5. 5243.

Miscellaneous databases

EvolutionaryTraceiQ8U0H6.

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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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(1998) [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(2005) [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(2010) [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(2011) [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(2007) [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(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR IN COMPLEX WITH RNP1 AND ZINC, COFACTOR, SUBUNIT, MUTAGENESIS OF ALA-14.

Entry informationi

Entry nameiRNP4_PYRFU
AccessioniPrimary (citable) accession number: Q8U0H6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 4, 2004
Last sequence update: May 31, 2002
Last modified: March 31, 2015
This is version 68 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

External Data

Dasty 3

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 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.