PPR74_ARATH
ID PPR74_ARATH Reviewed; 239 AA.
AC P0C7R1; Q9SX89;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 64.
DE RecName: Full=Pentatricopeptide repeat-containing protein DWY1, chloroplastic;
DE AltName: Full=DYW-domain protein 1 {ECO:0000303|PubMed:23001034};
DE Flags: Precursor;
GN Name=DYW1 {ECO:0000303|PubMed:23001034}; Synonyms=PCMP-H50;
GN OrderedLocusNames=At1g47580; ORFNames=F16N3.14;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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 3-239.
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
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, SUBCELLULAR LOCATION, INTERACTION WITH CRR4, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=23001034; DOI=10.1105/tpc.112.099507;
RA Boussardon C., Salone V., Avon A., Berthome R., Hammani K., Okuda K.,
RA Shikanai T., Small I., Lurin C.;
RT "Two interacting proteins are necessary for the editing of the NdhD-1 site
RT in Arabidopsis plastids.";
RL Plant Cell 24:3684-3694(2012).
RN [7]
RP 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).
RN [8]
RP COFACTOR.
RX PubMed=25041347; DOI=10.1111/nph.12928;
RA Boussardon C., Avon A., Kindgren P., Bond C.S., Challenor M., Lurin C.,
RA Small I.;
RT "The cytidine deaminase signature HxE(x)n CxxC of DYW1 binds zinc and is
RT necessary for RNA editing of ndhD-1.";
RL New Phytol. 203:1090-1095(2014).
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 site 1 of ndhD (ndhD-1 site corresponding to
CC cytidine-2), which is a plastid-encoded subunit of the NADH-
CC plastoquinone oxidoreductase. The interaction with CRR4 is required for
CC its function in editing the ndhD-1 site. {ECO:0000269|PubMed:23001034}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:24194514, ECO:0000269|PubMed:25041347};
CC Note=Binds 2 zinc ions per subunit. {ECO:0000269|PubMed:24194514};
CC -!- SUBUNIT: Interacts with CRR4. {ECO:0000269|PubMed:23001034}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:23001034}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but the mutant plants lack editing of the ndhD-1 site.
CC {ECO:0000269|PubMed:23001034}.
CC -!- MISCELLANEOUS: Unlike other RNA editing factors, DYW1 does not contain
CC identifiable PPR repeats but does contain E(+) and DYW motifs.
CC Therefore its association with CCR4, which lacks E(+) and DYW motifs,
CC but does contain PPR repeats, is required for its function in RNA
CC editing. {ECO:0000305|PubMed:23001034}.
CC -!- SIMILARITY: Belongs to the PPR family. PCMP-H subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD46029.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: At1g47578 and At1g47580.; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Pentatricopeptide repeat proteins;
CC URL="https://ppr.plantenergy.uwa.edu.au";
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DR EMBL; AC007519; AAD46029.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32190.1; -; Genomic_DNA.
DR EMBL; BX818700; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; D96516; D96516.
DR RefSeq; NP_175189.2; NM_103651.4.
DR AlphaFoldDB; P0C7R1; -.
DR SMR; P0C7R1; -.
DR BioGRID; 26392; 1.
DR STRING; 3702.AT1G47580.1; -.
DR PaxDb; P0C7R1; -.
DR PRIDE; P0C7R1; -.
DR ProteomicsDB; 226401; -.
DR EnsemblPlants; AT1G47580.1; AT1G47580.1; AT1G47580.
DR GeneID; 841167; -.
DR Gramene; AT1G47580.1; AT1G47580.1; AT1G47580.
DR KEGG; ath:AT1G47580; -.
DR Araport; AT1G47580; -.
DR TAIR; locus:2015378; AT1G47580.
DR eggNOG; KOG0325; Eukaryota.
DR eggNOG; KOG4197; Eukaryota.
DR HOGENOM; CLU_1311692_0_0_1; -.
DR OMA; CERETSS; -.
DR OrthoDB; 1170627at2759; -.
DR PhylomeDB; P0C7R1; -.
DR PRO; PR:P0C7R1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; P0C7R1; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:1900871; P:chloroplast mRNA modification; IMP:TAIR.
DR GO; GO:1900865; P:chloroplast RNA modification; IMP:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR InterPro; IPR032867; DYW_dom.
DR Pfam; PF14432; DYW_deaminase; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Metal-binding; mRNA processing; Plastid; Reference proteome;
KW RNA editing; Transit peptide; Zinc.
FT TRANSIT 1..35
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 36..239
FT /note="Pentatricopeptide repeat-containing protein DWY1,
FT chloroplastic"
FT /id="PRO_0000342815"
FT REGION 40..59
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 101..122
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 113..144
FT /note="Type E(+) motif"
FT /evidence="ECO:0000305|PubMed:23001034"
FT REGION 145..239
FT /note="Type DYW motif"
FT /evidence="ECO:0000305|PubMed:23001034"
FT COMPBIAS 40..55
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 239 AA; 26735 MW; 068591D56643B1E0 CRC64;
MALEAAFSMS FCSFSVPKAI FCERETSSFQ RITSRAKGIA GESQVQSSDG VETQVKETSP
KVFDKLPERN LDTWSGGRET ARGLSGSVVR NTVRKDTTLR HISPSSHSTK VRGDKPEISG
GEKKAIVDRS KAYVKLKSLG KEVRDAGYVP ETKYVLHDID EEAKEKALMH HSERLAIAFG
IINTPPGTTI RVMKNLRICG DCHNFIKILS SIEDREIIVR DNKRFHHFRD GNCSCGDYW
