PP320_ARATH
ID PP320_ARATH Reviewed; 871 AA.
AC Q9SN39; Q56XZ4;
DT 10-FEB-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 122.
DE RecName: Full=Pentatricopeptide repeat-containing protein DOT4, chloroplastic {ECO:0000305};
DE AltName: Full=Protein DEFECTIVELY ORGANIZED TRIBUTARIES 4 {ECO:0000303|PubMed:18643975};
DE AltName: Full=Protein FLAVODENTATA {ECO:0000303|PubMed:10394910};
DE Flags: Precursor;
GN Name=DOT4 {ECO:0000303|PubMed:18643975};
GN Synonyms=FLV {ECO:0000303|PubMed:10394910}, PCMP-H45;
GN OrderedLocusNames=At4g18750; ORFNames=F28A21.160;
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] OF 152-871.
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=10394910; DOI=10.1007/s004380050016;
RA Serrano-Cartagena J., Robles P., Ponce M.R., Micol J.L.;
RT "Genetic analysis of leaf form mutants from the Arabidopsis information
RT service collection.";
RL Mol. Gen. Genet. 261:725-739(1999).
RN [5]
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 [6]
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 [7]
RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=18643975; DOI=10.1111/j.1365-313x.2008.03595.x;
RA Petricka J.J., Clay N.K., Nelson T.M.;
RT "Vein patterning screens and the defectively organized tributaries mutants
RT in Arabidopsis thaliana.";
RL Plant J. 56:251-263(2008).
RN [8]
RP FUNCTION, AND COFACTOR.
RX PubMed=24194514; DOI=10.1074/jbc.m113.485755;
RA Hayes M.L., Giang K., Berhane B., Mulligan R.M.;
RT "Identification of two pentatricopeptide repeat genes required for RNA
RT editing and zinc binding by C-terminal cytidine deaminase-like domains.";
RL J. Biol. Chem. 288:36519-36529(2013).
CC -!- FUNCTION: Plays a major role in single RNA editing events in
CC chloroplasts. Acts as a site-recognition transacting factor involved in
CC the edition of the unique site (corresponding to cytidine-488) of
CC rpoC1, which is a plastid-encoded subunit of the chloroplast DNA-
CC directed RNA polymerase. May provide the catalytic activity for editing
CC site conversion (PubMed:24194514). Involved in leaf vasculature
CC patterning (PubMed:18643975). {ECO:0000269|PubMed:18643975,
CC ECO:0000269|PubMed:24194514}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q9SZT8};
CC Note=Binds 2 zinc ions per subunit. {ECO:0000250|UniProtKB:Q9SZT8};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Weakly expressed in leaves.
CC {ECO:0000269|PubMed:18643975}.
CC -!- DISRUPTION PHENOTYPE: Defects in venation pattern in leaves and
CC cotyledons. {ECO:0000269|PubMed:18643975}.
CC -!- SIMILARITY: Belongs to the PPR family. PCMP-H subfamily. {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Pentatricopeptide repeat proteins;
CC URL="https://ppr.plantenergy.uwa.edu.au";
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL035526; CAB37460.1; -; Genomic_DNA.
DR EMBL; AL161549; CAB78877.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84086.1; -; Genomic_DNA.
DR EMBL; AK221529; BAD94843.1; -; mRNA.
DR PIR; T04867; T04867.
DR RefSeq; NP_193610.1; NM_117991.3.
DR AlphaFoldDB; Q9SN39; -.
DR SMR; Q9SN39; -.
DR STRING; 3702.AT4G18750.1; -.
DR iPTMnet; Q9SN39; -.
DR PaxDb; Q9SN39; -.
DR PRIDE; Q9SN39; -.
DR ProteomicsDB; 248986; -.
DR EnsemblPlants; AT4G18750.1; AT4G18750.1; AT4G18750.
DR GeneID; 827609; -.
DR Gramene; AT4G18750.1; AT4G18750.1; AT4G18750.
DR KEGG; ath:AT4G18750; -.
DR Araport; AT4G18750; -.
DR TAIR; locus:2124137; AT4G18750.
DR eggNOG; KOG4197; Eukaryota.
DR HOGENOM; CLU_002706_15_0_1; -.
DR InParanoid; Q9SN39; -.
DR OMA; RNGYFSD; -.
DR OrthoDB; 1344243at2759; -.
DR PhylomeDB; Q9SN39; -.
DR PRO; PR:Q9SN39; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SN39; baseline and differential.
DR Genevisible; Q9SN39; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:1900865; P:chloroplast RNA modification; IMP:UniProtKB.
DR GO; GO:0010588; P:cotyledon vascular tissue pattern formation; IMP:TAIR.
DR GO; GO:0048366; P:leaf development; IMP:TAIR.
DR GO; GO:0010305; P:leaf vascular tissue pattern formation; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0010087; P:phloem or xylem histogenesis; IMP:TAIR.
DR Gene3D; 1.25.40.10; -; 5.
DR InterPro; IPR032867; DYW_dom.
DR InterPro; IPR002885; Pentatricopeptide_repeat.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR Pfam; PF14432; DYW_deaminase; 1.
DR Pfam; PF01535; PPR; 3.
DR Pfam; PF13041; PPR_2; 4.
DR TIGRFAMs; TIGR00756; PPR; 9.
DR PROSITE; PS51375; PPR; 18.
PE 2: Evidence at transcript level;
KW Chloroplast; Metal-binding; mRNA processing; Plastid; Reference proteome;
KW Repeat; RNA editing; RNA-binding; Transit peptide; Zinc.
FT TRANSIT 1..28
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 29..871
FT /note="Pentatricopeptide repeat-containing protein DOT4,
FT chloroplastic"
FT /id="PRO_0000363437"
FT REPEAT 60..94
FT /note="PPR 1"
FT REPEAT 96..127
FT /note="PPR 2"
FT REPEAT 128..158
FT /note="PPR 3"
FT REPEAT 159..193
FT /note="PPR 4"
FT REPEAT 194..228
FT /note="PPR 5"
FT REPEAT 229..259
FT /note="PPR 6"
FT REPEAT 260..294
FT /note="PPR 7"
FT REPEAT 295..329
FT /note="PPR 8"
FT REPEAT 330..360
FT /note="PPR 9"
FT REPEAT 361..395
FT /note="PPR 10"
FT REPEAT 396..430
FT /note="PPR 11"
FT REPEAT 431..465
FT /note="PPR 12"
FT REPEAT 466..497
FT /note="PPR 13"
FT REPEAT 498..532
FT /note="PPR 14"
FT REPEAT 533..563
FT /note="PPR 15"
FT REPEAT 564..598
FT /note="PPR 16"
FT REPEAT 599..629
FT /note="PPR 17"
FT REPEAT 635..665
FT /note="PPR 18"
FT REGION 670..745
FT /note="Type E motif"
FT REGION 746..776
FT /note="Type E(+) motif"
FT REGION 777..871
FT /note="Type DYW motif"
SQ SEQUENCE 871 AA; 97698 MW; C8AE13BF2589DF7A CRC64;
MAMLVTNLSS SSFCFFSSPH LQNQKEIRSG VRVRKYVIFN RASLRTVSDC VDSITTFDRS
VTDANTQLRR FCESGNLENA VKLLCVSGKW DIDPRTLCSV LQLCADSKSL KDGKEVDNFI
RGNGFVIDSN LGSKLSLMYT NCGDLKEASR VFDEVKIEKA LFWNILMNEL AKSGDFSGSI
GLFKKMMSSG VEMDSYTFSC VSKSFSSLRS VHGGEQLHGF ILKSGFGERN SVGNSLVAFY
LKNQRVDSAR KVFDEMTERD VISWNSIING YVSNGLAEKG LSVFVQMLVS GIEIDLATIV
SVFAGCADSR LISLGRAVHS IGVKACFSRE DRFCNTLLDM YSKCGDLDSA KAVFREMSDR
SVVSYTSMIA GYAREGLAGE AVKLFEEMEE EGISPDVYTV TAVLNCCARY RLLDEGKRVH
EWIKENDLGF DIFVSNALMD MYAKCGSMQE AELVFSEMRV KDIISWNTII GGYSKNCYAN
EALSLFNLLL EEKRFSPDER TVACVLPACA SLSAFDKGRE IHGYIMRNGY FSDRHVANSL
VDMYAKCGAL LLAHMLFDDI ASKDLVSWTV MIAGYGMHGF GKEAIALFNQ MRQAGIEADE
ISFVSLLYAC SHSGLVDEGW RFFNIMRHEC KIEPTVEHYA CIVDMLARTG DLIKAYRFIE
NMPIPPDATI WGALLCGCRI HHDVKLAEKV AEKVFELEPE NTGYYVLMAN IYAEAEKWEQ
VKRLRKRIGQ RGLRKNPGCS WIEIKGRVNI FVAGDSSNPE TENIEAFLRK VRARMIEEGY
SPLTKYALID AEEMEKEEAL CGHSEKLAMA LGIISSGHGK IIRVTKNLRV CGDCHEMAKF
MSKLTRREIV LRDSNRFHQF KDGHCSCRGF W
