RNP3_PYRHO
ID RNP3_PYRHO Reviewed; 212 AA.
AC O59543;
DT 13-APR-2004, 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 3 {ECO:0000255|HAMAP-Rule:MF_00756};
DE Short=RNase P component 3 {ECO:0000255|HAMAP-Rule:MF_00756};
DE EC=3.1.26.5 {ECO:0000255|HAMAP-Rule:MF_00756};
DE AltName: Full=Rpp30 {ECO:0000255|HAMAP-Rule:MF_00756};
GN Name=rnp3 {ECO:0000255|HAMAP-Rule:MF_00756}; OrderedLocusNames=PH1877;
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 (1.8 ANGSTROMS), AND MUTAGENESIS OF LYS-42; ARG-68;
RP ARG-87; ARG-90; ASP-98; ARG-107; HIS-114; LYS-123; LYS-158; ARG-176;
RP ASP-180 AND LYS-196.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=15184052; DOI=10.1016/j.bbrc.2004.05.055;
RA Takagi H., Watanabe M., Kakuta Y., Kamachi R., Numata T., Tanaka I.,
RA Kimura M.;
RT "Crystal structure of the ribonuclease P protein Ph1877p from
RT hyperthermophilic archaeon Pyrococcus horikoshii OT3.";
RL Biochem. Biophys. Res. Commun. 319:787-794(2004).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH RNP2, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=16430919; DOI=10.1016/j.jmb.2005.12.086;
RA Kawano S., Nakashima T., Kakuta Y., Tanaka I., Kimura M.;
RT "Crystal structure of protein Ph1481p in complex with protein Ph1877p of
RT archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer
RT formation of the holoenzyme.";
RL J. Mol. Biol. 357:583-591(2006).
CC -!- FUNCTION: Part of ribonuclease P, a protein complex that generates
CC mature tRNA molecules by cleaving their 5'-ends. Not absolutely
CC essential for activity in vitro, however it strongly stimulates
CC activity. Binds RNase P RNA. {ECO:0000255|HAMAP-Rule:MF_00756,
CC ECO:0000269|PubMed:12810070, ECO:0000269|PubMed:16574071,
CC ECO:0000269|PubMed:16829535}.
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_00756};
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 heterotetrameric subcomplex with Rnp2. 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:16430919,
CC ECO:0000269|PubMed:16574071, ECO:0000269|PubMed:16829535}.
CC -!- INTERACTION:
CC O59543; O59150: rnp2; NbExp=2; IntAct=EBI-2603192, EBI-2603177;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00756}.
CC -!- SIMILARITY: Belongs to the eukaryotic/archaeal RNase P protein
CC component 3 family. {ECO:0000255|HAMAP-Rule:MF_00756}.
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DR EMBL; BA000001; BAA30999.1; -; Genomic_DNA.
DR PIR; H71200; H71200.
DR PDB; 1V77; X-ray; 1.80 A; A=1-212.
DR PDB; 2CZV; X-ray; 2.00 A; A/B=1-212.
DR PDBsum; 1V77; -.
DR PDBsum; 2CZV; -.
DR AlphaFoldDB; O59543; -.
DR SMR; O59543; -.
DR IntAct; O59543; 1.
DR STRING; 70601.3258316; -.
DR EnsemblBacteria; BAA30999; BAA30999; BAA30999.
DR KEGG; pho:PH1877; -.
DR eggNOG; arCOG00307; Archaea.
DR OMA; WFDEVVF; -.
DR BRENDA; 3.1.26.5; 5244.
DR EvolutionaryTrace; O59543; -.
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:0001682; P:tRNA 5'-leader removal; IDA:UniProtKB.
DR HAMAP; MF_00756; RNase_P_3; 1.
DR InterPro; IPR016195; Pol/histidinol_Pase-like.
DR InterPro; IPR023539; RNase_P_comp-3_arc.
DR InterPro; IPR002738; RNase_P_p30.
DR Pfam; PF01876; RNase_P_p30; 1.
DR SUPFAM; SSF89550; SSF89550; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endonuclease; Hydrolase; Nuclease;
KW tRNA processing.
FT CHAIN 1..212
FT /note="Ribonuclease P protein component 3"
FT /id="PRO_0000140046"
FT MUTAGEN 42
FT /note="K->A: Fully reconstitutes RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 68
FT /note="R->A: 75% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 87
FT /note="R->A: Fully reconstitutes RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 90
FT /note="R->A: 45% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 98
FT /note="D->A: 80% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 107
FT /note="R->A: 45% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 114
FT /note="H->A: 75% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 123
FT /note="K->A: 45% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 158
FT /note="K->A: 75% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 176
FT /note="R->A: 45% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 180
FT /note="D->A: 50% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT MUTAGEN 196
FT /note="K->A: 45% reconstituted RNase P activity."
FT /evidence="ECO:0000269|PubMed:15184052"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:2CZV"
FT STRAND 10..14
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 17..26
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 28..38
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 42..52
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 55..61
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 64..73
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 75..82
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 86..94
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:1V77"
FT TURN 103..106
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 114..123
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 132..136
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 139..159
FT /evidence="ECO:0007829|PDB:1V77"
FT STRAND 163..166
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 192..197
FT /evidence="ECO:0007829|PDB:1V77"
FT TURN 198..200
FT /evidence="ECO:0007829|PDB:1V77"
FT HELIX 201..207
FT /evidence="ECO:0007829|PDB:1V77"
SQ SEQUENCE 212 AA; 24694 MW; 321490D4A2859C24 CRC64;
MVGGGGVKFI EMDIRDKEAY ELAKEWFDEV VVSIKFNEEV DKEKLREARK EYGKVAILLS
NPKPSLVRDT VQKFKSYLIY VESNDLRVIR YSIEKGVDAI ISPWVNRKDP GIDHVLAKLM
VKKNVALGFS LRPLLYSNPY ERANLLRFMM KAWKLVEKYK VRRFLTSSAQ EKWDVRYPRD
LISLGVVIGM EIPQAKASIS MYPEIILKRL KY
