DPD1_ARATH
ID DPD1_ARATH Reviewed; 316 AA.
AC Q682U6; Q681U1; Q8LBK8;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Exonuclease DPD1, chloroplastic/mitochondrial {ECO:0000303|PubMed:21521697};
DE EC=3.1.11.-;
DE AltName: Full=Mg2+-dependent DNA exonuclease {ECO:0000312|EMBL:AED93629.1};
DE AltName: Full=Protein DEFECTIVE IN POLLEN DNA DEGRADATION 1 {ECO:0000303|PubMed:21521697};
DE Flags: Precursor;
GN Name=DPD1 {ECO:0000303|PubMed:21521697};
GN OrderedLocusNames=At5g26940 {ECO:0000312|Araport:AT5G26940};
GN ORFNames=F2P16.200 {ECO:0000312|EMBL:AF007270};
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 {ECO:0000312|EMBL:BAD43034.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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].
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ARG-123; GLY-204 AND
RP ALA-236, SUBCELLULAR LOCATION, COFACTOR, TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. No-0;
RX PubMed=21521697; DOI=10.1105/tpc.111.084012;
RA Matsushima R., Tang L.Y., Zhang L., Yamada H., Twell D., Sakamoto W.;
RT "A conserved, Mg2+-dependent exonuclease degrades organelle DNA during
RT Arabidopsis pollen development.";
RL Plant Cell 23:1608-1624(2011).
RN [7]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=21852754; DOI=10.4161/psb.6.9.16595;
RA Tang L.Y., Sakamoto W.;
RT "Tissue-specific organelle DNA degradation mediated by DPD1 exonuclease.";
RL Plant Signal. Behav. 6:1391-1393(2011).
RN [8]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=22239102; DOI=10.1111/j.1365-313x.2012.04904.x;
RA Tang L.Y., Matsushima R., Sakamoto W.;
RT "Mutations defective in ribonucleotide reductase activity interfere with
RT pollen plastid DNA degradation mediated by DPD1 exonuclease.";
RL Plant J. 70:637-649(2012).
CC -!- FUNCTION: Exonuclease required for organelle DNA degradation during
CC pollen development. Plays non-essential roles in maternal inheritance.
CC May be part of the DNA salvage machinery. {ECO:0000269|PubMed:21521697,
CC ECO:0000269|PubMed:21852754, ECO:0000269|PubMed:22239102}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:21521697};
CC -!- ACTIVITY REGULATION: Inhibited by free nucleotide diphosphates (NDPs).
CC {ECO:0000269|PubMed:22239102}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:21521697}. Mitochondrion
CC {ECO:0000269|PubMed:21521697}.
CC -!- TISSUE SPECIFICITY: Highly expressed in mature pollen grains. Detected
CC in flowers, senescing leaves and roots. {ECO:0000269|PubMed:21521697,
CC ECO:0000269|PubMed:21852754}.
CC -!- DEVELOPMENTAL STAGE: Starts to express at the bicellular pollen stage,
CC with a peak at the tricellular pollen stage.
CC {ECO:0000269|PubMed:21521697}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:21521697}.
CC -!- MISCELLANEOUS: DPD1 homologs are present in flowering plants but not in
CC moss, green algae and animals. {ECO:0000305|PubMed:21852754}.
CC -!- SIMILARITY: Belongs to the exonuclease superfamily. TREX family.
CC {ECO:0000305}.
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; AF007270; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93629.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93630.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93631.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93632.1; -; Genomic_DNA.
DR EMBL; BT025876; ABF85778.1; -; mRNA.
DR EMBL; AK175271; BAD43034.1; -; mRNA.
DR EMBL; AK175526; BAD43289.1; -; mRNA.
DR EMBL; AY087151; AAM64709.1; -; mRNA.
DR PIR; T01771; T01771.
DR RefSeq; NP_198046.1; NM_122576.5.
DR RefSeq; NP_851082.1; NM_180751.2.
DR RefSeq; NP_851083.1; NM_180752.3.
DR RefSeq; NP_974842.1; NM_203113.3.
DR AlphaFoldDB; Q682U6; -.
DR SMR; Q682U6; -.
DR STRING; 3702.AT5G26940.2; -.
DR iPTMnet; Q682U6; -.
DR PaxDb; Q682U6; -.
DR PRIDE; Q682U6; -.
DR ProteomicsDB; 241245; -.
DR EnsemblPlants; AT5G26940.1; AT5G26940.1; AT5G26940.
DR EnsemblPlants; AT5G26940.2; AT5G26940.2; AT5G26940.
DR EnsemblPlants; AT5G26940.3; AT5G26940.3; AT5G26940.
DR EnsemblPlants; AT5G26940.4; AT5G26940.4; AT5G26940.
DR GeneID; 832752; -.
DR Gramene; AT5G26940.1; AT5G26940.1; AT5G26940.
DR Gramene; AT5G26940.2; AT5G26940.2; AT5G26940.
DR Gramene; AT5G26940.3; AT5G26940.3; AT5G26940.
DR Gramene; AT5G26940.4; AT5G26940.4; AT5G26940.
DR KEGG; ath:AT5G26940; -.
DR Araport; AT5G26940; -.
DR TAIR; locus:2148453; AT5G26940.
DR eggNOG; KOG4793; Eukaryota.
DR HOGENOM; CLU_060445_0_0_1; -.
DR InParanoid; Q682U6; -.
DR OMA; QCHVPNS; -.
DR OrthoDB; 1365966at2759; -.
DR PRO; PR:Q682U6; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q682U6; baseline and differential.
DR Genevisible; Q682U6; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IBA:GO_Central.
DR GO; GO:0004527; F:exonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IMP:TAIR.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR013520; Exonuclease_RNaseT/DNA_pol3.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR040393; TREX1/2.
DR PANTHER; PTHR13058; PTHR13058; 1.
DR Pfam; PF00929; RNase_T; 1.
DR SMART; SM00479; EXOIII; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Exonuclease; Hydrolase; Magnesium; Metal-binding;
KW Mitochondrion; Nuclease; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..63
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 64..316
FT /note="Exonuclease DPD1, chloroplastic/mitochondrial"
FT /evidence="ECO:0000255"
FT /id="PRO_0000430887"
FT DOMAIN 112..282
FT /note="Exonuclease"
FT /evidence="ECO:0000255"
FT ACT_SITE 269
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q91XB0"
FT BINDING 115
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q91XB0"
FT BINDING 115
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q91XB0"
FT BINDING 117
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q91XB0"
FT BINDING 274
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q91XB0"
FT MUTAGEN 123
FT /note="R->W: In dpd1-3; loss of activity."
FT /evidence="ECO:0000269|PubMed:21521697"
FT MUTAGEN 204
FT /note="G->S: In dpd1-2; loss of activity."
FT /evidence="ECO:0000269|PubMed:21521697"
FT MUTAGEN 236
FT /note="A->V: In dpd1-1; loss of activity."
FT /evidence="ECO:0000269|PubMed:21521697"
FT CONFLICT 3
FT /note="I -> V (in Ref. 5; AAM64709)"
FT CONFLICT 124
FT /note="K -> E (in Ref. 4; BAD43289)"
SQ SEQUENCE 316 AA; 35248 MW; 7B9669C163B62DB9 CRC64;
MCISISQVSR LRIHSFGSSC CERVHGWIKN SSSLKLLDVR ASSVDGKARW IRRNVSTTTQ
GSRSNTKSSV LGGTVPVTRI IDEESRTKVQ PFGNLQQRLA QDKDLSKLLT VIVSDLETTG
LHRKNERIIE IAAQDIAGGG YSTFQTLVNP GVVPITNAHI HGIRNDMVCR PEVPRMEELI
PIFLRYVESR QKPGGYVMLV AHNGKSFDFQ FLINEFNRCS YEIPHNWLLL DSLPLARENM
KSVEPTVKLS SSLEALADYY SLTREGDAHR ALSDVLLLSK VFQKLTIDLK LSLSDLVLRC
HTASDISAAM AKNKKA
