RNP1_PYRHO
ID RNP1_PYRHO Reviewed; 127 AA.
AC O59425;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 25-MAY-2022, entry version 119.
DE RecName: Full=Ribonuclease P protein component 1 {ECO:0000255|HAMAP-Rule:MF_00754};
DE Short=RNase P component 1 {ECO:0000255|HAMAP-Rule:MF_00754};
DE EC=3.1.26.5 {ECO:0000255|HAMAP-Rule:MF_00754};
DE AltName: Full=Rpp29 {ECO:0000255|HAMAP-Rule:MF_00754};
GN Name=rnp1 {ECO:0000255|HAMAP-Rule:MF_00754}; OrderedLocusNames=PH1771;
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 (2.0 ANGSTROMS) OF 32-127.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=15317976; DOI=10.1261/rna.7560904;
RA Numata T., Ishimatsu I., Kakuta Y., Tanaka I., Kimura M.;
RT "Crystal structure of archaeal ribonuclease P protein Ph1771p from
RT Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P
RT protein Rpp29.";
RL RNA 10:1423-1432(2004).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) IN COMPLEX WITH RNP4, FUNCTION,
RP SUBUNIT, AND MUTAGENESIS OF 1-MET--ARG-31; GLU-47; GLU-73; ARG-75; LYS-90;
RP PHE-95; ARG-115; 118-MET--TRP-127; LYS-121; 121-LYS-LYS-122; LYS-122 AND
RP 124-TRP--TRP-127.
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 (RNase P), a protein complex that
CC generates mature tRNA molecules by cleaving their 5'-ends. Binds RNase
CC P RNA. {ECO:0000269|PubMed:12810070, 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_00754};
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 Rnp4. 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:16574071,
CC ECO:0000269|PubMed:16829535, ECO:0000269|PubMed:18929577}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00754}.
CC -!- SIMILARITY: Belongs to the eukaryotic/archaeal RNase P protein
CC component 1 family. {ECO:0000255|HAMAP-Rule:MF_00754}.
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DR EMBL; BA000001; BAA30886.1; -; Genomic_DNA.
DR PIR; G71186; G71186.
DR PDB; 1V76; X-ray; 2.00 A; A/B=32-127.
DR PDB; 2ZAE; X-ray; 2.21 A; A/C=1-127.
DR PDBsum; 1V76; -.
DR PDBsum; 2ZAE; -.
DR AlphaFoldDB; O59425; -.
DR SMR; O59425; -.
DR IntAct; O59425; 1.
DR STRING; 70601.3258203; -.
DR EnsemblBacteria; BAA30886; BAA30886; BAA30886.
DR KEGG; pho:PH1771; -.
DR eggNOG; arCOG00784; Archaea.
DR OMA; WHELIGL; -.
DR BRENDA; 3.1.26.5; 5244.
DR EvolutionaryTrace; O59425; -.
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:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0001682; P:tRNA 5'-leader removal; IDA:UniProtKB.
DR Gene3D; 2.30.30.210; -; 1.
DR HAMAP; MF_00754; RNase_P_1; 1.
DR InterPro; IPR036980; RNase_P/MRP_Rpp29_sf.
DR InterPro; IPR023538; RNP1.
DR InterPro; IPR023534; Rof/RNase_P-like.
DR InterPro; IPR002730; Rpp29/RNP1.
DR Pfam; PF01868; RNase_P-MRP_p29; 1.
DR SMART; SM00538; POP4; 1.
DR SUPFAM; SSF101744; SSF101744; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endonuclease; Hydrolase; Nuclease;
KW tRNA processing.
FT CHAIN 1..127
FT /note="Ribonuclease P protein component 1"
FT /id="PRO_0000128437"
FT MUTAGEN 1..31
FT /note="Missing: Does not reconstitute RNase P activity, no
FT longer interacts with Rnp4."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 47
FT /note="E->A: Fully reconstitutes RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 73
FT /note="E->A: 40% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 75
FT /note="R->A: 40% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 90
FT /note="K->A: 10% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 95
FT /note="F->A: 75% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 115
FT /note="R->A: 75% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 118..127
FT /note="Missing: Does not reconstitute RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 121..122
FT /note="KK->AA: 60% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 121
FT /note="K->A: 90% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 122
FT /note="K->A: Fully reconstitutes RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT MUTAGEN 124..127
FT /note="Missing: Fully reconstitutes RNase P activity."
FT /evidence="ECO:0000269|PubMed:18929577"
FT HELIX 21..23
FT /evidence="ECO:0007829|PDB:2ZAE"
FT HELIX 27..30
FT /evidence="ECO:0007829|PDB:2ZAE"
FT TURN 31..33
FT /evidence="ECO:0007829|PDB:2ZAE"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:1V76"
FT STRAND 52..60
FT /evidence="ECO:0007829|PDB:1V76"
FT HELIX 61..63
FT /evidence="ECO:0007829|PDB:1V76"
FT STRAND 67..73
FT /evidence="ECO:0007829|PDB:1V76"
FT STRAND 75..90
FT /evidence="ECO:0007829|PDB:1V76"
FT STRAND 93..98
FT /evidence="ECO:0007829|PDB:1V76"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:1V76"
FT HELIX 109..112
FT /evidence="ECO:0007829|PDB:1V76"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:1V76"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:1V76"
SQ SEQUENCE 127 AA; 15054 MW; 840FE2A1234FF0AD CRC64;
MRRNSKERKN RATRRSQGSY QEIIGRTWIF RGAHRGRVTR RNIIWHELIG LRVRIVGSTH
PAFVGIEGYV IDETRNMLVI AGDRIWKVPK DVCIFEFEAD DGTKIKIPGE RLVGRPEMRL
KKRWKKW
