PP319_ARATH
ID PP319_ARATH Reviewed; 617 AA.
AC Q0WNP3; O49520;
DT 10-FEB-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=Pentatricopeptide repeat-containing protein At4g18520, chloroplastic;
DE AltName: Full=Protein PIGMENT-DEFICIENT MUTANT 1 {ECO:0000303|Ref.6};
DE AltName: Full=Protein SEEDLING LETHAL 1 {ECO:0000303|PubMed:24144791};
DE Flags: Precursor;
GN Name=PCMP-A2;
GN Synonyms=PDM1 {ECO:0000303|Ref.6}, SEL1 {ECO:0000303|PubMed:24144791};
GN OrderedLocusNames=At4g18520; ORFNames=F28J12.180;
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].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA 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 GENE FAMILY.
RX PubMed=10809006; DOI=10.1023/a:1006352315928;
RA Aubourg S., Boudet N., Kreis M., Lecharny A.;
RT "In Arabidopsis thaliana, 1% of the genome codes for a novel protein family
RT unique to plants.";
RL Plant Mol. Biol. 42:603-613(2000).
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.
RX DOI=10.1007/s11434-010-4040-4;
RA Wu H., Zhang L.;
RT "The PPR protein PDM1 is involved in the processing of rpoA pre-mRNA in
RT Arabidopsis thaliana.";
RL Chin. Sci. Bull. 55:3485-3489(2010).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX DOI=10.1007/s11434-012-5278-9;
RA Wu H., Zhang L., Yin Q.Q., Cui Y.L., Zhang G.R., Zhang H.D., Wang X.M.,
RA Yang Z.N.;
RT "The Arabidopsis pentatricopeptide repeat protein PDM1 is associated with
RT the intergenic sequence of S11-rpoA for rpoA monocistronic RNA cleavage.";
RL Chin. Sci. Bull. 57:3452-3459(2012).
RN [8]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=24144791; DOI=10.1104/pp.113.227199;
RA Pyo Y.J., Kwon K.C., Kim A., Cho M.H.;
RT "Seedling Lethal1, a pentatricopeptide repeat protein lacking an E/E+ or
RT DYW domain in Arabidopsis, is involved in plastid gene expression and early
RT chloroplast development.";
RL Plant Physiol. 163:1844-1858(2013).
RN [9]
RP FUNCTION, AND INTERACTION WITH MORF8/RIP1; MORF2/RIP2 AND MORF9/RIP9.
RX PubMed=26123918; DOI=10.1007/s11120-015-0171-4;
RA Zhang H.D., Cui Y.L., Huang C., Yin Q.Q., Qin X.M., Xu T., He X.F.,
RA Zhang Y., Li Z.R., Yang Z.N.;
RT "PPR protein PDM1/SEL1 is involved in RNA editing and splicing of plastid
RT genes in Arabidopsis thaliana.";
RL Photosyn. Res. 126:311-321(2015).
CC -!- FUNCTION: Required for proper chloroplast development (Ref.7,
CC PubMed:24144791). Involved in the regulation of plastid gene expression
CC probably through regulation of plastid-encoded polymerase (PEP)
CC dependent chloroplast transcription (PubMed:24144791). Required for RNA
CC editing of several chloroplastic transcripts, especially accD
CC transcripts (PubMed:24144791, PubMed:26123918). Required for processing
CC of the chloroplastic rpoA pre-mRNA (Ref.6, Ref.7). Required for the
CC monocistronic rpoA transcript processing from the rpl23-rpl2-rps19-
CC rpl22-rps3-rpl16-rpl14-rps8-rpl36-rps11-rpoA polycistron. Binds the
CC intergenic sequence of rps11-rpoA for rpoA monocistronic RNA cleavage
CC (Ref.7). {ECO:0000269|PubMed:24144791, ECO:0000269|PubMed:26123918,
CC ECO:0000269|Ref.6, ECO:0000269|Ref.7}.
CC -!- SUBUNIT: Interacts with MORF8/RIP1, MORF2/RIP2 and MORF9/RIP9.
CC {ECO:0000269|PubMed:26123918}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000269|Ref.7}.
CC -!- TISSUE SPECIFICITY: Expressed specifically in aerial greening tissues,
CC such as cotyledons, rosette leaves, cauline leaves, stems, sepals,
CC stamens, carpels and siliques. {ECO:0000269|PubMed:24144791}.
CC -!- DISRUPTION PHENOTYPE: Albino lethal phenotype with severe chloroplast
CC development defects. {ECO:0000269|PubMed:24144791, ECO:0000269|Ref.7}.
CC -!- SIMILARITY: Belongs to the PPR family. PCMP-A subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA16732.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78854.1; 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; AL021710; CAA16732.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161548; CAB78854.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84057.1; -; Genomic_DNA.
DR EMBL; AK229394; BAF01256.1; -; mRNA.
DR PIR; T04548; T04548.
DR RefSeq; NP_193587.4; NM_117966.5.
DR AlphaFoldDB; Q0WNP3; -.
DR SMR; Q0WNP3; -.
DR BioGRID; 12877; 3.
DR STRING; 3702.AT4G18520.1; -.
DR PaxDb; Q0WNP3; -.
DR PRIDE; Q0WNP3; -.
DR ProteomicsDB; 249223; -.
DR EnsemblPlants; AT4G18520.1; AT4G18520.1; AT4G18520.
DR GeneID; 827584; -.
DR Gramene; AT4G18520.1; AT4G18520.1; AT4G18520.
DR KEGG; ath:AT4G18520; -.
DR Araport; AT4G18520; -.
DR TAIR; locus:2124603; AT4G18520.
DR eggNOG; KOG4197; Eukaryota.
DR HOGENOM; CLU_002706_0_1_1; -.
DR InParanoid; Q0WNP3; -.
DR OMA; KRNTVTW; -.
DR OrthoDB; 1344243at2759; -.
DR PhylomeDB; Q0WNP3; -.
DR PRO; PR:Q0WNP3; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q0WNP3; baseline and differential.
DR Genevisible; Q0WNP3; AT.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:1900865; P:chloroplast RNA modification; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0009451; P:RNA modification; IBA:GO_Central.
DR GO; GO:0008380; P:RNA splicing; IMP:TAIR.
DR Gene3D; 1.25.40.10; -; 5.
DR InterPro; IPR002885; Pentatricopeptide_repeat.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR Pfam; PF01535; PPR; 6.
DR Pfam; PF13041; PPR_2; 2.
DR TIGRFAMs; TIGR00756; PPR; 8.
DR PROSITE; PS51375; PPR; 13.
PE 1: Evidence at protein level;
KW Chloroplast; mRNA processing; Plastid; Reference proteome; Repeat;
KW RNA-binding; Transit peptide.
FT TRANSIT 1..19
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 20..617
FT /note="Pentatricopeptide repeat-containing protein
FT At4g18520, chloroplastic"
FT /id="PRO_0000363436"
FT REPEAT 116..146
FT /note="PPR 1"
FT REPEAT 147..181
FT /note="PPR 2"
FT REPEAT 183..217
FT /note="PPR 3"
FT REPEAT 222..247
FT /note="PPR 4"
FT REPEAT 248..282
FT /note="PPR 5"
FT REPEAT 283..317
FT /note="PPR 6"
FT REPEAT 318..348
FT /note="PPR 7"
FT REPEAT 349..383
FT /note="PPR 8"
FT REPEAT 384..418
FT /note="PPR 9"
FT REPEAT 419..449
FT /note="PPR 10"
FT REPEAT 450..484
FT /note="PPR 11"
FT REPEAT 485..519
FT /note="PPR 12"
FT REPEAT 520..550
FT /note="PPR 13"
FT REPEAT 551..585
FT /note="PPR 14"
SQ SEQUENCE 617 AA; 69275 MW; 0F279AA6FBA72D6A CRC64;
MFSLSLIQPR LRISEIPVTQ SYKSPTICYS SDSRTKREEQ RHVRLPGFRL VSGKRASFDS
GFSGFKGENV NQDDSSSFDS ERVDYALLAE WLQSSNGMRL IKRIHAMALK CFDDQVIYFG
NNLISSCVRL GDLVYARKVF DSMPEKNTVT WTAMIDGYLK YGLEDEAFAL FEDYVKHGIR
FTNERMFVCL LNLCSRRAEF ELGRQVHGNM VKVGVGNLIV ESSLVYFYAQ CGELTSALRA
FDMMEEKDVI SWTAVISACS RKGHGIKAIG MFIGMLNHWF LPNEFTVCSI LKACSEEKAL
RFGRQVHSLV VKRMIKTDVF VGTSLMDMYA KCGEISDCRK VFDGMSNRNT VTWTSIIAAH
AREGFGEEAI SLFRIMKRRH LIANNLTVVS ILRACGSVGA LLLGKELHAQ IIKNSIEKNV
YIGSTLVWLY CKCGESRDAF NVLQQLPSRD VVSWTAMISG CSSLGHESEA LDFLKEMIQE
GVEPNPFTYS SALKACANSE SLLIGRSIHS IAKKNHALSN VFVGSALIHM YAKCGFVSEA
FRVFDSMPEK NLVSWKAMIM GYARNGFCRE ALKLMYRMEA EGFEVDDYIF ATILSTCGDI
ELDEAVESSA TCYLETS
