RNP4_PYRFU
ID RNP4_PYRFU Reviewed; 117 AA.
AC Q8U0H6;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=Ribonuclease P protein component 4 {ECO:0000255|HAMAP-Rule:MF_00757};
DE Short=RNase P component 4 {ECO:0000255|HAMAP-Rule:MF_00757};
DE EC=3.1.26.5 {ECO:0000255|HAMAP-Rule:MF_00757};
DE AltName: Full=Rpp21 {ECO:0000255|HAMAP-Rule:MF_00757};
GN Name=rnp4 {ECO:0000255|HAMAP-Rule:MF_00757}; OrderedLocusNames=PF1613;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=17053064; DOI=10.1073/pnas.0608000103;
RA Tsai H.Y., Pulukkunat D.K., Woznick W.K., Gopalan V.;
RT "Functional reconstitution and characterization of Pyrococcus furiosus
RT RNase P.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:16147-16152(2006).
RN [3]
RP FUNCTION, INTERACTION WITH RNP1, AND SUBUNIT.
RX PubMed=21683084; DOI=10.1016/j.jmb.2011.05.012;
RA Chen W.Y., Xu Y., Cho I.M., Oruganti S.V., Foster M.P., Gopalan V.;
RT "Cooperative RNP assembly: complementary rescue of structural defects by
RT protein and RNA subunits of archaeal RNase P.";
RL J. Mol. Biol. 411:368-383(2011).
RN [4]
RP FUNCTION, INTERACTION WITH RNP1, AND SUBUNIT.
RX PubMed=22298511; DOI=10.1093/nar/gks013;
RA Chen W.Y., Singh D., Lai L.B., Stiffler M.A., Lai H.D., Foster M.P.,
RA Gopalan V.;
RT "Fidelity of tRNA 5'-maturation: a possible basis for the functional
RT dependence of archaeal and eukaryal RNase P on multiple protein
RT cofactors.";
RL Nucleic Acids Res. 40:4666-4680(2012).
RN [5]
RP STRUCTURE BY NMR IN COMPLEX WITH ZINC, INTERACTION WITH RNP1, SUBUNIT, AND
RP COFACTOR.
RX PubMed=18922021; DOI=10.1021/bi8015982;
RA Amero C.D., Boomershine W.P., Xu Y., Foster M.;
RT "Solution structure of Pyrococcus furiosus RPP21, a component of the
RT archaeal RNase P holoenzyme, and interactions with its RPP29 protein
RT partner.";
RL Biochemistry 47:11704-11710(2008).
RN [6]
RP STRUCTURE BY NMR IN COMPLEX WITH RNP1 AND ZINC, COFACTOR, SUBUNIT, AND
RP MUTAGENESIS OF ALA-14.
RX PubMed=19733182; DOI=10.1016/j.jmb.2009.08.068;
RA Xu Y., Amero C.D., Pulukkunat D.K., Gopalan V., Foster M.P.;
RT "Solution structure of an archaeal RNase P binary protein complex:
RT formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29
RT is accompanied by coupled protein folding and highlights critical features
RT for protein-protein and protein-RNA interactions.";
RL J. Mol. Biol. 393:1043-1055(2009).
CC -!- FUNCTION: Part of ribonuclease P, a protein complex that generates
CC mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic,
CC but its KM for pre-tRNA is 170-fold decreased in the presence of the 4
CC known protein subunits (Rnp1-4). The protein subunits also decrease the
CC amount of Mg(2+) needed for activity. {ECO:0000255|HAMAP-Rule:MF_00757,
CC ECO:0000269|PubMed:17053064, ECO:0000269|PubMed:21683084,
CC ECO:0000269|PubMed:22298511}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of RNA, removing 5'-extranucleotides
CC from tRNA precursor.; EC=3.1.26.5; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00757, ECO:0000269|PubMed:17053064};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00757,
CC ECO:0000269|PubMed:18922021, ECO:0000269|PubMed:19733182};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00757,
CC ECO:0000269|PubMed:18922021, ECO:0000269|PubMed:19733182};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.18 uM for E.coli pre-tRNA(Tyr) {ECO:0000269|PubMed:17053064};
CC Note=kcat is 9.5 min(-1). For enzyme reconstituted with RNA and 4
CC known subunits (Rnp1-4).;
CC -!- SUBUNIT: Consists of a catalytic RNA component and at least 4 protein
CC subunits. Forms a subcomplex with Rnp1 which stimulates the catalytic
CC RNA. {ECO:0000269|PubMed:17053064, ECO:0000269|PubMed:18922021,
CC ECO:0000269|PubMed:19733182, ECO:0000269|PubMed:21683084,
CC ECO:0000269|PubMed:22298511}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00757}.
CC -!- SIMILARITY: Belongs to the eukaryotic/archaeal RNase P protein
CC component 4 family. {ECO:0000255|HAMAP-Rule:MF_00757}.
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DR EMBL; AE009950; AAL81737.1; -; Genomic_DNA.
DR RefSeq; WP_011012760.1; NZ_CP023154.1.
DR PDB; 2K3R; NMR; -; A=1-117.
DR PDB; 2KI7; NMR; -; B=1-117.
DR PDBsum; 2K3R; -.
DR PDBsum; 2KI7; -.
DR AlphaFoldDB; Q8U0H6; -.
DR BMRB; Q8U0H6; -.
DR SMR; Q8U0H6; -.
DR STRING; 186497.PF1613; -.
DR EnsemblBacteria; AAL81737; AAL81737; PF1613.
DR GeneID; 41713438; -.
DR KEGG; pfu:PF1613; -.
DR PATRIC; fig|186497.12.peg.1680; -.
DR eggNOG; arCOG04345; Archaea.
DR HOGENOM; CLU_079140_3_1_2; -.
DR OMA; HVVITCL; -.
DR OrthoDB; 128960at2157; -.
DR PhylomeDB; Q8U0H6; -.
DR BRENDA; 3.1.26.5; 5243.
DR EvolutionaryTrace; Q8U0H6; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0030677; C:ribonuclease P complex; IEA:UniProtKB-UniRule.
DR GO; GO:0004526; F:ribonuclease P activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0001682; P:tRNA 5'-leader removal; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00757; RNase_P_4; 1.
DR InterPro; IPR016432; RNP4.
DR InterPro; IPR007175; Rpr2/Snm1/Rpp21.
DR Pfam; PF04032; Rpr2; 1.
DR PIRSF; PIRSF004878; RNase_P_4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endonuclease; Hydrolase; Metal-binding; Nuclease;
KW Reference proteome; tRNA processing; Zinc.
FT CHAIN 1..117
FT /note="Ribonuclease P protein component 4"
FT /id="PRO_0000153859"
FT BINDING 63
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00757,
FT ECO:0000269|PubMed:18922021, ECO:0000269|PubMed:19733182"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00757,
FT ECO:0000269|PubMed:18922021, ECO:0000269|PubMed:19733182"
FT BINDING 92
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00757,
FT ECO:0000269|PubMed:18922021, ECO:0000269|PubMed:19733182"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00757,
FT ECO:0000269|PubMed:18922021, ECO:0000269|PubMed:19733182"
FT MUTAGEN 14
FT /note="A->V: 3-fold reduced binding to Rnp1."
FT /evidence="ECO:0000269|PubMed:19733182"
FT HELIX 16..31
FT /evidence="ECO:0007829|PDB:2K3R"
FT HELIX 33..50
FT /evidence="ECO:0007829|PDB:2K3R"
FT TURN 57..60
FT /evidence="ECO:0007829|PDB:2K3R"
FT TURN 64..66
FT /evidence="ECO:0007829|PDB:2K3R"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:2K3R"
FT STRAND 75..81
FT /evidence="ECO:0007829|PDB:2K3R"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:2K3R"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:2K3R"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:2K3R"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:2K3R"
SQ SEQUENCE 117 AA; 14303 MW; 876CD8CC664F3F38 CRC64;
MAKYNEKKEK KRIAKERIDI LFSLAERVFP YSPELAKRYV ELALLVQQKA KVKIPRKWKR
RYCKKCHAFL VPGINARVRL RQKRMPHIVV KCLECGHIMR YPYIKEIKKR RKEKMEY
