RNP4_PYRHO
ID RNP4_PYRHO Reviewed; 120 AA.
AC O59248;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 113.
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=PH1601;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND RNA-BINDING.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=12810070; DOI=10.1016/s0006-291x(03)01034-9;
RA Kouzuma Y., Mizoguchi M., Takagi H., Fukuhara H., Tsukamoto M., Numata T.,
RA Kimura M.;
RT "Reconstitution of archaeal ribonuclease P from RNA and four protein
RT components.";
RL Biochem. Biophys. Res. Commun. 306:666-673(2003).
RN [3]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=16574071; DOI=10.1016/j.bbrc.2006.02.192;
RA Fukuhara H., Kifusa M., Watanabe M., Terada A., Honda T., Numata T.,
RA Kakuta Y., Kimura M.;
RT "A fifth protein subunit Ph1496p elevates the optimum temperature for the
RT ribonuclease P activity from Pyrococcus horikoshii OT3.";
RL Biochem. Biophys. Res. Commun. 343:956-964(2006).
RN [4]
RP FUNCTION, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=16829535; DOI=10.1093/jb/mvj144;
RA Terada A., Honda T., Fukuhara H., Hada K., Kimura M.;
RT "Characterization of the archaeal ribonuclease P proteins from Pyrococcus
RT horikoshii OT3.";
RL J. Biochem. 140:293-298(2006).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH ZN(2+), FUNCTION,
RP COFACTOR, AND MUTAGENESIS OF ARG-22; TYR-44; ARG-65; 68-CYS--CYS-71;
RP LYS-69; ARG-84; ARG-86; 97-CYS--CYS-100 AND ARG-105.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=16142906; DOI=10.1021/bi050738z;
RA Kakuta Y., Ishimatsu I., Numata T., Kimura K., Yao M., Tanaka I.,
RA Kimura M.;
RT "Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus
RT horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P
RT protein Rpp21.";
RL Biochemistry 44:12086-12093(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) IN COMPLEX WITH RNP1 AND ZN(2+),
RP FUNCTION, COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=18929577; DOI=10.1016/j.jmb.2008.09.056;
RA Honda T., Kakuta Y., Kimura K., Saho J., Kimura M.;
RT "Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29
RT that is a key core component for the assembly of active ribonuclease P.";
RL J. Mol. Biol. 384:652-662(2008).
CC -!- FUNCTION: Part of ribonuclease P, a protein complex that generates
CC mature tRNA molecules by cleaving their 5'-ends. Binds RNase P RNA.
CC {ECO:0000255|HAMAP-Rule:MF_00757, ECO:0000269|PubMed:12810070,
CC ECO:0000269|PubMed:16142906, ECO:0000269|PubMed:16574071,
CC ECO:0000269|PubMed:16829535, ECO:0000269|PubMed:18929577}.
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};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00757,
CC ECO:0000269|PubMed:16142906, ECO:0000269|PubMed:18929577};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00757,
CC ECO:0000269|PubMed:16142906, ECO:0000269|PubMed:18929577};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 70 degrees Celsius.
CC {ECO:0000269|PubMed:12810070, ECO:0000269|PubMed:16574071};
CC -!- SUBUNIT: Consists of a catalytic RNA component and at least 5 protein
CC subunits. Forms a heterodimeric subcomplex with Rnp1. Reconstituted
CC enzyme missing individual protein subunits is suboptimally active,
CC showing each subunit contributes to optimization of activity.
CC {ECO:0000269|PubMed:12810070, ECO:0000269|PubMed:16142906,
CC ECO:0000269|PubMed:16574071, ECO:0000269|PubMed:16829535,
CC ECO:0000269|PubMed:18929577}.
CC -!- INTERACTION:
CC O59248; O59150: rnp2; NbExp=3; IntAct=EBI-2641275, EBI-2603177;
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; BA000001; BAA30713.1; -; Genomic_DNA.
DR PIR; A71039; A71039.
DR RefSeq; WP_010885676.1; NC_000961.1.
DR PDB; 1X0T; X-ray; 1.60 A; A=1-120.
DR PDB; 2ZAE; X-ray; 2.21 A; B/D=1-120.
DR PDBsum; 1X0T; -.
DR PDBsum; 2ZAE; -.
DR AlphaFoldDB; O59248; -.
DR SMR; O59248; -.
DR IntAct; O59248; 2.
DR STRING; 70601.3258030; -.
DR EnsemblBacteria; BAA30713; BAA30713; BAA30713.
DR GeneID; 1442455; -.
DR KEGG; pho:PH1601; -.
DR eggNOG; arCOG04345; Archaea.
DR OMA; HVVITCL; -.
DR OrthoDB; 128960at2157; -.
DR BRENDA; 3.1.26.5; 5244.
DR EvolutionaryTrace; O59248; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0030677; C:ribonuclease P complex; IDA:UniProtKB.
DR GO; GO:0004526; F:ribonuclease P activity; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0001682; P:tRNA 5'-leader removal; IDA:UniProtKB.
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 tRNA processing; Zinc.
FT CHAIN 1..120
FT /note="Ribonuclease P protein component 4"
FT /id="PRO_0000153860"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 71
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 97
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT MUTAGEN 22
FT /note="R->A: 40% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 44
FT /note="Y->A: 40% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 65
FT /note="R->A: 70% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 68..71
FT /note="CKRC->SKRS: Does not reconstitute RNase P activity.
FT Protein destabilized."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 69
FT /note="K->A: 10% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 84
FT /note="R->A: 50% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 86
FT /note="R->A: 20% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 97..100
FT /note="CLEC->SLES: Does not reconstitute RNase P activity.
FT Protein destabilized."
FT /evidence="ECO:0000269|PubMed:16142906"
FT MUTAGEN 105
FT /note="R->A: Does not reconstitute RNase P activity."
FT /evidence="ECO:0000269|PubMed:16142906"
FT HELIX 5..34
FT /evidence="ECO:0007829|PDB:1X0T"
FT HELIX 38..55
FT /evidence="ECO:0007829|PDB:1X0T"
FT TURN 61..65
FT /evidence="ECO:0007829|PDB:1X0T"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:1X0T"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:1X0T"
FT STRAND 80..86
FT /evidence="ECO:0007829|PDB:1X0T"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:1X0T"
FT STRAND 92..97
FT /evidence="ECO:0007829|PDB:1X0T"
FT TURN 98..100
FT /evidence="ECO:0007829|PDB:1X0T"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:1X0T"
SQ SEQUENCE 120 AA; 14589 MW; 2AC453B35C964AE6 CRC64;
MVDIVKRRDW EKKEKKKIAI ERIDTLFTLA ERVARYSPDL AKRYVELALE IQKKAKVKIP
RKWKRRYCKR CHTFLIPGVN ARVRLRTKRM PHVVITCLEC GYIMRYPYLR EVKQKRKKAT
