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Exonuclease DPD1, chloroplastic/mitochondrial (EC 3.1.11.-) (Mg2 -dependent DNA exonuclease) (Protein DEFECTIVE IN POLLEN DNA DEGRADATION 1)

 DPD1_ARATH              Reviewed;         316 AA.
Q682U6; Q681U1; Q8LBK8;
29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
11-OCT-2004, sequence version 1.
25-APR-2018, entry version 115.
RecName: Full=Exonuclease DPD1, chloroplastic/mitochondrial {ECO:0000303|PubMed:21521697};
EC=3.1.11.-;
AltName: Full=Mg2+-dependent DNA exonuclease {ECO:0000312|EMBL:AED93629.1};
AltName: Full=Protein DEFECTIVE IN POLLEN DNA DEGRADATION 1 {ECO:0000303|PubMed:21521697};
Flags: Precursor;
Name=DPD1 {ECO:0000303|PubMed:21521697};
OrderedLocusNames=At5g26940 {ECO:0000312|Araport:AT5G26940};
ORFNames=F2P16.200 {ECO:0000312|EMBL:AF007270};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702 {ECO:0000312|EMBL:BAD43034.1};
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130714; DOI=10.1038/35048507;
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K.,
Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S.,
Nakazaki N., Naruo K., Okumura S., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M.,
Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R.,
Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J.,
Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M.,
Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M.,
Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P.,
Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C.,
Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N.,
Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J.,
Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S.,
Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W.,
Ramsperger U., Wedler H., Balke K., Wedler E., Peters S.,
van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R.,
Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S.,
Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W.,
Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H.,
Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.;
"Sequence and analysis of chromosome 5 of the plant Arabidopsis
thaliana.";
Nature 408:823-826(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
"Arabidopsis ORF clones.";
Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[6]
FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ARG-123; GLY-204 AND
ALA-236, SUBCELLULAR LOCATION, COFACTOR, TISSUE SPECIFICITY, AND
DEVELOPMENTAL STAGE.
STRAIN=cv. Columbia, and cv. No-0;
PubMed=21521697; DOI=10.1105/tpc.111.084012;
Matsushima R., Tang L.Y., Zhang L., Yamada H., Twell D., Sakamoto W.;
"A conserved, Mg2+-dependent exonuclease degrades organelle DNA during
Arabidopsis pollen development.";
Plant Cell 23:1608-1624(2011).
[7]
FUNCTION, AND TISSUE SPECIFICITY.
PubMed=21852754; DOI=10.4161/psb.6.9.16595;
Tang L.Y., Sakamoto W.;
"Tissue-specific organelle DNA degradation mediated by DPD1
exonuclease.";
Plant Signal. Behav. 6:1391-1393(2011).
[8]
FUNCTION, AND ENZYME REGULATION.
PubMed=22239102; DOI=10.1111/j.1365-313X.2012.04904.x;
Tang L.Y., Matsushima R., Sakamoto W.;
"Mutations defective in ribonucleotide reductase activity interfere
with pollen plastid DNA degradation mediated by DPD1 exonuclease.";
Plant J. 70:637-649(2012).
-!- FUNCTION: Exonuclease required for organelle DNA degradation
during pollen development. Plays non-essential roles in maternal
inheritance. May be part of the DNA salvage machinery.
{ECO:0000269|PubMed:21521697, ECO:0000269|PubMed:21852754,
ECO:0000269|PubMed:22239102}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:21521697};
-!- ENZYME REGULATION: Inhibited by free nucleotide diphosphates
(NDPs). {ECO:0000269|PubMed:22239102}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast
{ECO:0000269|PubMed:21521697}. Mitochondrion
{ECO:0000269|PubMed:21521697}.
-!- TISSUE SPECIFICITY: Highly expressed in mature pollen grains.
Detected in flowers, senescing leaves and roots.
{ECO:0000269|PubMed:21521697, ECO:0000269|PubMed:21852754}.
-!- DEVELOPMENTAL STAGE: Starts to express at the bicellular pollen
stage, with a peak at the tricellular pollen stage.
{ECO:0000269|PubMed:21521697}.
-!- DISRUPTION PHENOTYPE: No visible phenotype.
{ECO:0000269|PubMed:21521697}.
-!- MISCELLANEOUS: DPD1 homologs are present in flowering plants but
not in moss, green algae and animals.
{ECO:0000305|PubMed:21852754}.
-!- SIMILARITY: Belongs to the exonuclease superfamily. TREX family.
{ECO:0000305}.
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EMBL; AF007270; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CP002688; AED93629.1; -; Genomic_DNA.
EMBL; CP002688; AED93630.1; -; Genomic_DNA.
EMBL; CP002688; AED93631.1; -; Genomic_DNA.
EMBL; CP002688; AED93632.1; -; Genomic_DNA.
EMBL; BT025876; ABF85778.1; -; mRNA.
EMBL; AK175271; BAD43034.1; -; mRNA.
EMBL; AK175526; BAD43289.1; -; mRNA.
EMBL; AY087151; AAM64709.1; -; mRNA.
PIR; T01771; T01771.
RefSeq; NP_198046.1; NM_122576.5.
RefSeq; NP_851082.1; NM_180751.2.
RefSeq; NP_851083.1; NM_180752.3.
RefSeq; NP_974842.1; NM_203113.3.
UniGene; At.20000; -.
ProteinModelPortal; Q682U6; -.
SMR; Q682U6; -.
STRING; 3702.AT5G26940.1; -.
iPTMnet; Q682U6; -.
PaxDb; Q682U6; -.
EnsemblPlants; AT5G26940.1; AT5G26940.1; AT5G26940.
EnsemblPlants; AT5G26940.2; AT5G26940.2; AT5G26940.
EnsemblPlants; AT5G26940.3; AT5G26940.3; AT5G26940.
EnsemblPlants; AT5G26940.4; AT5G26940.4; AT5G26940.
GeneID; 832752; -.
Gramene; AT5G26940.1; AT5G26940.1; AT5G26940.
Gramene; AT5G26940.2; AT5G26940.2; AT5G26940.
Gramene; AT5G26940.3; AT5G26940.3; AT5G26940.
Gramene; AT5G26940.4; AT5G26940.4; AT5G26940.
KEGG; ath:AT5G26940; -.
Araport; AT5G26940; -.
TAIR; locus:2148453; AT5G26940.
eggNOG; KOG4793; Eukaryota.
eggNOG; ENOG4111YSP; LUCA.
HOGENOM; HOG000095607; -.
InParanoid; Q682U6; -.
OMA; CHTASDI; -.
OrthoDB; EOG09360FXS; -.
PRO; PR:Q682U6; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q682U6; baseline and differential.
Genevisible; Q682U6; AT.
GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
GO; GO:0005739; C:mitochondrion; IDA:TAIR.
GO; GO:0009536; C:plastid; IDA:TAIR.
GO; GO:0004527; F:exonuclease activity; IDA:TAIR.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IMP:TAIR.
Gene3D; 3.30.420.10; -; 1.
InterPro; IPR013520; Exonuclease_RNaseT/DNA_pol3.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
Pfam; PF00929; RNase_T; 1.
SMART; SM00479; EXOIII; 1.
SUPFAM; SSF53098; SSF53098; 1.
1: Evidence at protein level;
Chloroplast; Complete proteome; Exonuclease; Hydrolase; Magnesium;
Metal-binding; Mitochondrion; Nuclease; Plastid; Reference proteome;
Transit peptide.
TRANSIT 1 63 Chloroplast and mitochondrion.
{ECO:0000255}.
CHAIN 64 316 Exonuclease DPD1,
chloroplastic/mitochondrial.
{ECO:0000255}.
/FTId=PRO_0000430887.
DOMAIN 112 282 Exonuclease. {ECO:0000255}.
ACT_SITE 269 269 Proton donor/acceptor.
{ECO:0000250|UniProtKB:Q91XB0}.
METAL 115 115 Magnesium 1.
{ECO:0000250|UniProtKB:Q91XB0}.
METAL 115 115 Magnesium 2.
{ECO:0000250|UniProtKB:Q91XB0}.
METAL 117 117 Magnesium 1.
{ECO:0000250|UniProtKB:Q91XB0}.
METAL 274 274 Magnesium 1.
{ECO:0000250|UniProtKB:Q91XB0}.
MUTAGEN 123 123 R->W: In dpd1-3; loss of activity.
{ECO:0000269|PubMed:21521697}.
MUTAGEN 204 204 G->S: In dpd1-2; loss of activity.
{ECO:0000269|PubMed:21521697}.
MUTAGEN 236 236 A->V: In dpd1-1; loss of activity.
{ECO:0000269|PubMed:21521697}.
CONFLICT 3 3 I -> V (in Ref. 5; AAM64709).
CONFLICT 124 124 K -> E (in Ref. 4; BAD43289).
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


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