PRRP3_ARATH
ID PRRP3_ARATH Reviewed; 576 AA.
AC F4JKB6; O49713; Q0WKW9; Q0WVS1;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Proteinaceous RNase P 3;
DE EC=3.1.26.5;
GN Name=PRORP3; OrderedLocusNames=At4g21900; ORFNames=T8O5.110;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Morosawa T.,
RA Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K.,
RA Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K.,
RA Akiyama K., Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
RA Hayashizaki Y., Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP IDENTIFICATION, AND SUBCELLULAR LOCATION.
RX PubMed=20473316; DOI=10.1038/nsmb.1812;
RA Gobert A., Gutmann B., Taschner A., Goessringer M., Holzmann J.,
RA Hartmann R.K., Rossmanith W., Giege P.;
RT "A single Arabidopsis organellar protein has RNase P activity.";
RL Nat. Struct. Mol. Biol. 17:740-744(2010).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, MUTAGENESIS OF
RP 480-ASP-ASP-481, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=22549728; DOI=10.1101/gad.189514.112;
RA Gutmann B., Gobert A., Giege P.;
RT "PRORP proteins support RNase P activity in both organelles and the nucleus
RT in Arabidopsis.";
RL Genes Dev. 26:1022-1027(2012).
CC -!- FUNCTION: Endonuclease RNase P responsible for the 5' maturation of
CC tRNA precursors. Also involved in the maturation of mRNA and small
CC nucleolar RNA (snoRNA). {ECO:0000269|PubMed:22549728}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of RNA, removing 5'-extranucleotides
CC from tRNA precursor.; EC=3.1.26.5;
CC Evidence={ECO:0000269|PubMed:22549728};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q66GI4};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q66GI4};
CC Note=Binds 2 Mg(2+) or Mg(2+) ions per subunit.
CC {ECO:0000250|UniProtKB:Q66GI4};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.3 uM for tRNA(Gln) precursor {ECO:0000269|PubMed:22549728};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20473316}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy with
CC PRORP2. Prorp2 and prorp3 double mutant is lethal.
CC {ECO:0000269|PubMed:22549728}.
CC -!- SIMILARITY: Belongs to the PPR family. P subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAE98777.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAF02238.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};
CC Sequence=CAA17157.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79145.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL021890; CAA17157.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161556; CAB79145.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84521.1; -; Genomic_DNA.
DR EMBL; AK226669; BAE98777.1; ALT_INIT; mRNA.
DR EMBL; AK230440; BAF02238.1; ALT_SEQ; mRNA.
DR PIR; T05472; T05472.
DR RefSeq; NP_193921.2; NM_118311.7.
DR AlphaFoldDB; F4JKB6; -.
DR SMR; F4JKB6; -.
DR STRING; 3702.AT4G21900.1; -.
DR PaxDb; F4JKB6; -.
DR PRIDE; F4JKB6; -.
DR ProteomicsDB; 226477; -.
DR EnsemblPlants; AT4G21900.1; AT4G21900.1; AT4G21900.
DR GeneID; 828279; -.
DR Gramene; AT4G21900.1; AT4G21900.1; AT4G21900.
DR KEGG; ath:AT4G21900; -.
DR Araport; AT4G21900; -.
DR TAIR; locus:2141662; AT4G21900.
DR eggNOG; KOG1347; Eukaryota.
DR HOGENOM; CLU_014066_2_0_1; -.
DR InParanoid; F4JKB6; -.
DR OMA; TEASHGC; -.
DR OrthoDB; 1247650at2759; -.
DR BRENDA; 3.1.26.5; 399.
DR PRO; PR:F4JKB6; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JKB6; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004526; F:ribonuclease P activity; IDA:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR GO; GO:0043144; P:sno(s)RNA processing; IMP:UniProtKB.
DR GO; GO:0001682; P:tRNA 5'-leader removal; IDA:UniProtKB.
DR Gene3D; 1.25.40.10; -; 1.
DR InterPro; IPR033443; PPR_long.
DR InterPro; IPR031595; PRORP_C.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR Pfam; PF17177; PPR_long; 1.
DR Pfam; PF16953; PRORP; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease; Nucleus;
KW Reference proteome; Repeat; tRNA processing; Zinc.
FT CHAIN 1..576
FT /note="Proteinaceous RNase P 3"
FT /id="PRO_0000420274"
FT REPEAT 88..123
FT /note="PPR 1"
FT REPEAT 129..166
FT /note="PPR 2"
FT REPEAT 167..201
FT /note="PPR 3"
FT REPEAT 204..238
FT /note="PPR 4"
FT DOMAIN 335..570
FT /note="PRORP"
FT REGION 65..88
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 340
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 343
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 402
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 480
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 481
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 499
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 553
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT BINDING 570
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q66GI4"
FT MUTAGEN 480..481
FT /note="DD->AA: Loss of activity."
FT /evidence="ECO:0000269|PubMed:22549728"
FT CONFLICT 185
FT /note="D -> G (in Ref. 3; BAF02238)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 576 AA; 64396 MW; 10A34B9C5F166DAD CRC64;
MKLKKPSLPS SLLCAVPPCL SQIRLLIPRR VRVSSSTFAN AKLVTLRNHT VNLHIYYCSM
AGTDNRRSRH DDESPKNPNK KKKGNRNPEK SLLINLHSCS KRKDLSAALA LYDAAITSSD
IRLNQQHFQS LLYLCSAFIS DPSLQTVAID RGFQIFDRMV SSGISPNESS VTAVARLAAA
KGDGDYAFKL VKDLVAVGGV SVPRLRTYAP ALLCFCDTLE AEKGYEVEDH MDASGIVLEE
AEISALLKVS AATGRENKVY RYLQKLRECV GCVSEETSKA IEEWFYGVKA SEVSDNGIGS
DIELLRAAVL KNGGGWHGLG WVGEGKWIVK KGNVSSAGKC LSCDEHLACV DTNEVETEDF
VNSLVTLAME RKAKMNSCEP MADFSEFQEW LEKHGDYEAI LDGANIGLYQ QNFADGGFSL
PQLEAVVKEL YNKSGSKKQP LILLHKKRVN ALLENPNHRN LVEEWINNNV LYATPPGSND
DWYWLYAAAK LKCLLVTNDE MRDHIFELLS NSFFQKWKER HQVRFTFVKG CLKLEMPPPF
SVVIQESEKG SWHVPITSQD KEESLRSWMC ITRQSS
