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   27-MAR-2024, entry version 72.
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.F4JKB6; -.
DR   PaxDb; 3702-AT4G21900-1; -.
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; AT4G21900; PRORP3.
DR   eggNOG; KOG1347; Eukaryota.
DR   HOGENOM; CLU_014066_2_0_1; -.
DR   InParanoid; F4JKB6; -.
DR   OMA; YAVETHM; -.
DR   OrthoDB; 47419at2759; -.
DR   BRENDA; 3.1.26.5; 399.
DR   SABIO-RK; F4JKB6; -.
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   CDD; cd18671; PIN_PRORP-Zc3h12a-like; 1.
DR   Gene3D; 3.40.50.11980; -; 1.
DR   Gene3D; 1.25.40.10; Tetratricopeptide repeat domain; 1.
DR   InterPro; IPR033443; PPR_long.
DR   InterPro; IPR031595; PRORP_C.
DR   InterPro; IPR011990; TPR-like_helical_dom_sf.
DR   PANTHER; PTHR13547:SF20; PROTEINACEOUS RNASE P 3; 1.
DR   PANTHER; PTHR13547; UNCHARACTERIZED; 1.
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
//