PRRP1_ARATH
ID PRRP1_ARATH Reviewed; 572 AA.
AC Q66GI4; Q8RWW5; Q9SKX7;
DT 16-DEC-2008, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Proteinaceous RNase P 1, chloroplastic/mitochondrial;
DE EC=3.1.26.5 {ECO:0000269|PubMed:20473316, ECO:0000269|PubMed:22549728, ECO:0000269|PubMed:22991464};
DE AltName: Full=Pentatricopeptide repeat-containing protein At2g32230;
DE Flags: Precursor;
GN Name=PRORP1; OrderedLocusNames=At2g32230; ORFNames=F22D22.2;
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Cheuk R.F., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP GENE FAMILY.
RX PubMed=15269332; DOI=10.1105/tpc.104.022236;
RA Lurin C., Andres C., Aubourg S., Bellaoui M., Bitton F., Bruyere C.,
RA Caboche M., Debast C., Gualberto J., Hoffmann B., Lecharny A., Le Ret M.,
RA Martin-Magniette M.-L., Mireau H., Peeters N., Renou J.-P., Szurek B.,
RA Taconnat L., Small I.;
RT "Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins
RT reveals their essential role in organelle biogenesis.";
RL Plant Cell 16:2089-2103(2004).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE,
RP AND MUTAGENESIS OF 474-ASP-ASP-475.
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 [7]
RP FUNCTION.
RX PubMed=20660484; DOI=10.1093/nar/gkq646;
RA Placido A., Sieber F., Gobert A., Gallerani R., Giege P.,
RA Marechal-Drouard L.;
RT "Plant mitochondria use two pathways for the biogenesis of tRNAHis.";
RL Nucleic Acids Res. 38:7711-7717(2010).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP ALA-70.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
RN [10] {ECO:0007744|PDB:4G23, ECO:0007744|PDB:4G24, ECO:0007744|PDB:4G25, ECO:0007744|PDB:4G26}
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 77-572 IN COMPLEX WITH MANGANESE
RP AND ZINC, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF
RP ASP-399; ASP-474; ASP-475 AND ASP-493.
RX PubMed=22991464; DOI=10.1073/pnas.1209062109;
RA Howard M.J., Lim W.H., Fierke C.A., Koutmos M.;
RT "Mitochondrial ribonuclease P structure provides insight into the evolution
RT of catalytic strategies for precursor-tRNA 5' processing.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:16149-16154(2012).
CC -!- FUNCTION: Endonuclease RNase P responsible for the 5' maturation of
CC tRNA precursors. Preferentially cleaves at the unusual cleavage site,
CC but also able to cleave at the classical cleavage site. Also involved
CC in the maturation of mRNAs in mitochondria.
CC {ECO:0000269|PubMed:20473316, ECO:0000269|PubMed:20660484,
CC ECO:0000269|PubMed:22549728, ECO:0000269|PubMed:22991464}.
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:20473316, ECO:0000269|PubMed:22549728,
CC ECO:0000269|PubMed:22991464};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000305|PubMed:22991464};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000305|PubMed:22991464};
CC Note=Binds 2 Mg(2+) or Mg(2+) ions per subunit.
CC {ECO:0000305|PubMed:22991464};
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:20473316,
CC ECO:0000305|PubMed:25732537}. Plastid, chloroplast
CC {ECO:0000269|PubMed:20473316}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethality when homozygous.
CC {ECO:0000269|PubMed:20473316}.
CC -!- SIMILARITY: Belongs to the PPR family. P subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD15382.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Pentatricopeptide repeat proteins;
CC URL="https://ppr.plantenergy.uwa.edu.au";
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DR EMBL; AC006223; AAD15382.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC08652.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM62476.1; -; Genomic_DNA.
DR EMBL; AY091059; AAM13880.1; -; mRNA.
DR EMBL; BT015418; AAU05541.1; -; mRNA.
DR PIR; E84730; E84730.
DR RefSeq; NP_001324632.1; NM_001336377.1.
DR RefSeq; NP_850186.1; NM_179855.3.
DR PDB; 4G23; X-ray; 1.98 A; A=77-572.
DR PDB; 4G24; X-ray; 1.95 A; A=77-572.
DR PDB; 4G25; X-ray; 2.00 A; A=77-572.
DR PDB; 4G26; X-ray; 1.75 A; A=77-572.
DR PDB; 6BV5; X-ray; 1.79 A; A=77-572.
DR PDB; 6BV6; X-ray; 2.20 A; A=77-572.
DR PDB; 6BV8; X-ray; 2.10 A; A=77-572.
DR PDB; 6BV9; X-ray; 2.10 A; A=77-572.
DR PDB; 6LVR; X-ray; 2.85 A; A/C=84-294.
DR PDBsum; 4G23; -.
DR PDBsum; 4G24; -.
DR PDBsum; 4G25; -.
DR PDBsum; 4G26; -.
DR PDBsum; 6BV5; -.
DR PDBsum; 6BV6; -.
DR PDBsum; 6BV8; -.
DR PDBsum; 6BV9; -.
DR PDBsum; 6LVR; -.
DR AlphaFoldDB; Q66GI4; -.
DR SMR; Q66GI4; -.
DR STRING; 3702.AT2G32230.1; -.
DR PaxDb; Q66GI4; -.
DR PRIDE; Q66GI4; -.
DR ProteomicsDB; 226475; -.
DR EnsemblPlants; AT2G32230.1; AT2G32230.1; AT2G32230.
DR EnsemblPlants; AT2G32230.2; AT2G32230.2; AT2G32230.
DR GeneID; 817782; -.
DR Gramene; AT2G32230.1; AT2G32230.1; AT2G32230.
DR Gramene; AT2G32230.2; AT2G32230.2; AT2G32230.
DR KEGG; ath:AT2G32230; -.
DR Araport; AT2G32230; -.
DR TAIR; locus:2045432; AT2G32230.
DR eggNOG; KOG1347; Eukaryota.
DR HOGENOM; CLU_014066_2_0_1; -.
DR InParanoid; Q66GI4; -.
DR OMA; CIDINPV; -.
DR OrthoDB; 1247650at2759; -.
DR PhylomeDB; Q66GI4; -.
DR BRENDA; 3.1.26.5; 399.
DR PRO; PR:Q66GI4; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q66GI4; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004526; F:ribonuclease P activity; IDA:TAIR.
DR GO; GO:0001682; P:tRNA 5'-leader removal; IMP:TAIR.
DR GO; GO:0008033; P:tRNA processing; IDA:TAIR.
DR Gene3D; 1.25.40.10; -; 1.
DR InterPro; IPR002885; Pentatricopeptide_repeat.
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.
DR PROSITE; PS51375; PPR; 3.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Mitochondrion; Nuclease; Plastid; Reference proteome; Repeat;
KW Transit peptide; tRNA processing; Zinc.
FT TRANSIT 1..70
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 71..572
FT /note="Proteinaceous RNase P 1,
FT chloroplastic/mitochondrial"
FT /id="PRO_0000356038"
FT REPEAT 96..130
FT /note="PPR 1"
FT REPEAT 136..174
FT /note="PPR 2"
FT REPEAT 175..209
FT /note="PPR 3"
FT REPEAT 210..244
FT /note="PPR 4"
FT DOMAIN 338..565
FT /note="PRORP"
FT BINDING 344
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:22991464,
FT ECO:0007744|PDB:4G23, ECO:0007744|PDB:4G24,
FT ECO:0007744|PDB:4G25, ECO:0007744|PDB:4G26"
FT BINDING 347
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:22991464,
FT ECO:0007744|PDB:4G23, ECO:0007744|PDB:4G24,
FT ECO:0007744|PDB:4G25, ECO:0007744|PDB:4G26"
FT BINDING 399
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:22991464"
FT BINDING 474
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:22991464"
FT BINDING 475
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:22991464,
FT ECO:0007744|PDB:4G24"
FT BINDING 493
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:22991464,
FT ECO:0007744|PDB:4G24"
FT BINDING 548
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:22991464,
FT ECO:0007744|PDB:4G23, ECO:0007744|PDB:4G24,
FT ECO:0007744|PDB:4G25, ECO:0007744|PDB:4G26"
FT BINDING 565
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:22991464,
FT ECO:0007744|PDB:4G23, ECO:0007744|PDB:4G24,
FT ECO:0007744|PDB:4G25, ECO:0007744|PDB:4G26"
FT MUTAGEN 399
FT /note="D->N: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:22991464"
FT MUTAGEN 474..475
FT /note="DD->AA: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20473316"
FT MUTAGEN 474
FT /note="D->N: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:22991464"
FT MUTAGEN 475
FT /note="D->N: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:22991464"
FT MUTAGEN 493
FT /note="D->N: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:22991464"
FT CONFLICT 250
FT /note="A -> V (in Ref. 3; AAM13880)"
FT /evidence="ECO:0000305"
FT HELIX 96..106
FT /evidence="ECO:0007829|PDB:4G26"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 113..126
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 132..142
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 155..169
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 176..189
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 192..204
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 211..223
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 227..239
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 246..258
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 262..275
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 277..279
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 281..292
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 294..297
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 306..316
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 317..319
FT /evidence="ECO:0007829|PDB:6BV5"
FT STRAND 331..336
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:4G26"
FT TURN 345..347
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 358..375
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 378..389
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 395..399
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 400..405
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 413..426
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 434..438
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 439..442
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 445..447
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 450..461
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 465..468
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 474..485
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 488..490
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 498..503
FT /evidence="ECO:0007829|PDB:4G26"
FT TURN 504..506
FT /evidence="ECO:0007829|PDB:4G26"
FT HELIX 507..515
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 516..522
FT /evidence="ECO:0007829|PDB:4G26"
FT TURN 523..525
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 526..530
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 547..551
FT /evidence="ECO:0007829|PDB:4G26"
FT TURN 556..558
FT /evidence="ECO:0007829|PDB:4G26"
FT STRAND 563..568
FT /evidence="ECO:0007829|PDB:4G26"
SQ SEQUENCE 572 AA; 64877 MW; 80857002D71F42FA CRC64;
MLRLTCFTPS FSRACCPLFA MMLKVPSVHL HHPRFSPFRF YHTSLLVKGT RDRRLILVER
SRHLCTLPLA AAKQSAASPS ENLSRKAKKK AIQQSPEALL KQKLDMCSKK GDVLEALRLY
DEARRNGVQL SQYHYNVLLY VCSLAEAATE SSPNPGLSRG FDIFKQMIVD KVVPNEATFT
NGARLAVAKD DPEMAFDMVK QMKAFGIQPR LRSYGPALFG FCRKGDADKA YEVDAHMVES
EVVPEEPELA ALLKVSMDTK NADKVYKTLQ RLRDLVRQVS KSTFDMIEEW FKSEVATKTG
VKKWDVKKIR DAVVSGGGGW HGQGWLGTGK WNVKRTEMDE NGVCKCCKEK LVCIDINPVE
TETFAASLTR LACEREVKAN FNQFQEWLER HGPFDAVIDG ANMGLVNQRS FSFFQLNNTV
QRCQQISPSK RLPLVILHKS RVNGGPATYP KNRALLEKWK NAGALYATPP GSNDDWYWLY
AAVSCKCLLV TNDEMRDHLF QLLGNSFFPR WKEKHQVRIS VTREDGLKLN MPPPYSIVIQ
ESEDGTWHVP MSVEDDLQTS RQWLCAKRSK TP
