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D-lactate dehydrogenase [cytochrome], mitochondrial (AtD-LDH) (EC 1.1.2.4) (D-lactate ferricytochrome C oxidoreductase) (Glycolate deshydrogenase)

 DLD_ARATH               Reviewed;         567 AA.
Q94AX4; Q9FG12;
20-APR-2010, integrated into UniProtKB/Swiss-Prot.
01-DEC-2001, sequence version 1.
07-JUN-2017, entry version 91.
RecName: Full=D-lactate dehydrogenase [cytochrome], mitochondrial;
Short=AtD-LDH;
EC=1.1.2.4;
AltName: Full=D-lactate ferricytochrome C oxidoreductase;
AltName: Full=Glycolate deshydrogenase;
Flags: Precursor;
Name=DLD; Synonyms=GDH; OrderedLocusNames=At5g06580;
ORFNames=F15M7.11;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases.
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
FUNCTION, ENZYME REGULATION, TISSUE SPECIFICITY, INDUCTION, AND
SUBCELLULAR LOCATION.
PubMed=14966218; DOI=10.1093/jxb/erh079;
Bari R., Kebeish R., Kalamajka R., Rademacher T., Peterhansel C.;
"A glycolate dehydrogenase in the mitochondria of Arabidopsis
thaliana.";
J. Exp. Bot. 55:623-630(2004).
[5]
FUNCTION, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
DISRUPTION PHENOTYPE.
PubMed=19586914; DOI=10.1074/jbc.M109.021253;
Engqvist M., Drincovich M.F., Flugge U.I., Maurino V.G.;
"Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with
catalytic capacities to participate in the last reactions of the
methylglyoxal and beta-oxidation pathways.";
J. Biol. Chem. 284:25026-25037(2009).
-!- FUNCTION: Catalyzes the stereospecific oxidation of D-lactate to
pyruvate. Involved in the detoxification of methylglyoxal and D-
lactate, but probably not involved in the metabolization of
glycolate. {ECO:0000269|PubMed:14966218,
ECO:0000269|PubMed:19586914}.
-!- CATALYTIC ACTIVITY: (R)-lactate + 2 ferricytochrome c = pyruvate +
2 ferrocytochrome c + 2 H(+).
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000269|PubMed:19586914};
Note=Binds 1 FAD per monomer. {ECO:0000269|PubMed:19586914};
-!- ENZYME REGULATION: Inhibited by cyanide ions.
{ECO:0000269|PubMed:14966218}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=61 uM for D-2-hydroxybutyrate (with cytochrome c as acceptor
molecule) {ECO:0000269|PubMed:19586914};
KM=164 uM for D-lactate (with cytochrome c as acceptor molecule)
{ECO:0000269|PubMed:19586914};
KM=4486 uM for L-lactate (with cytochrome c as acceptor
molecule) {ECO:0000269|PubMed:19586914};
KM=8871 uM for D-glycerate (with cytochrome c as acceptor
molecule) {ECO:0000269|PubMed:19586914};
KM=432 uM for glycolate (with cytochrome c as acceptor molecule)
{ECO:0000269|PubMed:19586914};
KM=317 uM for D-lactate (with DCIP as acceptor molecule)
{ECO:0000269|PubMed:19586914};
KM=7134 uM for L-lactate (with DCIP as acceptor molecule)
{ECO:0000269|PubMed:19586914};
KM=596 uM for glycolate (with DCIP as acceptor molecule)
{ECO:0000269|PubMed:19586914};
pH dependence:
Optimum pH is 8-9. {ECO:0000269|PubMed:19586914};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19586914}.
-!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14966218}.
-!- TISSUE SPECIFICITY: Expressed in leaves, stems, flowers and roots.
{ECO:0000269|PubMed:14966218}.
-!- INDUCTION: By light. {ECO:0000269|PubMed:14966218}.
-!- DISRUPTION PHENOTYPE: No visible phenotype when grown under
standard conditions, but developmental retardation and lethality
when grown in presence of methylglyoxal or D-lactate.
{ECO:0000269|PubMed:19586914}.
-!- SIMILARITY: Belongs to the FAD-binding oxidoreductase/transferase
type 4 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAB11407.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AP002543; BAB11407.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002688; AED91037.1; -; Genomic_DNA.
EMBL; AY045641; AAK73999.1; -; mRNA.
RefSeq; NP_568170.1; NM_120741.3.
UniGene; At.9066; -.
ProteinModelPortal; Q94AX4; -.
STRING; 3702.AT5G06580.1; -.
SwissPalm; Q94AX4; -.
PaxDb; Q94AX4; -.
EnsemblPlants; AT5G06580.1; AT5G06580.1; AT5G06580.
GeneID; 830546; -.
Gramene; AT5G06580.1; AT5G06580.1; AT5G06580.
KEGG; ath:AT5G06580; -.
Araport; AT5G06580; -.
TAIR; locus:2144093; AT5G06580.
eggNOG; KOG1231; Eukaryota.
eggNOG; COG0277; LUCA.
HOGENOM; HOG000230995; -.
InParanoid; Q94AX4; -.
KO; K00102; -.
OMA; TPRTCGE; -.
OrthoDB; EOG0936092F; -.
PhylomeDB; Q94AX4; -.
BioCyc; ARA:AT5G06580-MONOMER; -.
BioCyc; MetaCyc:AT5G06580-MONOMER; -.
PRO; PR:Q94AX4; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q94AX4; baseline and differential.
Genevisible; Q94AX4; AT.
GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
GO; GO:0005524; F:ATP binding; IDA:TAIR.
GO; GO:0004458; F:D-lactate dehydrogenase (cytochrome) activity; IDA:TAIR.
GO; GO:0008720; F:D-lactate dehydrogenase activity; IMP:TAIR.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:UniProtKB.
GO; GO:0019154; F:glycolate dehydrogenase activity; IDA:TAIR.
GO; GO:0008891; F:glycolate oxidase activity; IGI:TAIR.
GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
GO; GO:0051596; P:methylglyoxal catabolic process; IMP:UniProtKB.
Gene3D; 1.10.45.10; -; 1.
Gene3D; 3.30.43.10; -; 1.
Gene3D; 3.30.465.10; -; 1.
InterPro; IPR016169; CO_DH_flavot_FAD-bd_sub2.
InterPro; IPR016166; FAD-bd_2.
InterPro; IPR016167; FAD-bd_2_sub1.
InterPro; IPR016164; FAD-linked_Oxase-like_C.
InterPro; IPR004113; FAD-linked_oxidase_C.
InterPro; IPR006094; Oxid_FAD_bind_N.
InterPro; IPR016171; Vanillyl_alc_oxidase_C-sub2.
Pfam; PF02913; FAD-oxidase_C; 1.
Pfam; PF01565; FAD_binding_4; 1.
SUPFAM; SSF55103; SSF55103; 1.
SUPFAM; SSF56176; SSF56176; 1.
PROSITE; PS51387; FAD_PCMH; 1.
1: Evidence at protein level;
Complete proteome; FAD; Flavoprotein; Mitochondrion; Oxidoreductase;
Reference proteome; Transit peptide.
TRANSIT 1 56 Mitochondrion. {ECO:0000255}.
CHAIN 57 567 D-lactate dehydrogenase [cytochrome],
mitochondrial.
/FTId=PRO_0000393388.
DOMAIN 142 319 FAD-binding PCMH-type.
{ECO:0000255|PROSITE-ProRule:PRU00718}.
SEQUENCE 567 AA; 62176 MW; 780E506EB06C4E88 CRC64;
MAFASKFARS KTILSFLRPC RQLHSTPKST GDVTVLSPVK GRRRLPTCWS SSLFPLAIAA
SATSFAYLNL SNPSISESSS ALDSRDITVG GKDSTEAVVK GEYKQVPKEL ISQLKTILED
NLTTDYDERY FHGKPQNSFH KAVNIPDVVV FPRSEEEVSK ILKSCNEYKV PIVPYGGATS
IEGHTLAPKG GVCIDMSLMK RVKALHVEDM DVIVEPGIGW LELNEYLEEY GLFFPLDPGP
GASIGGMCAT RCSGSLAVRY GTMRDNVISL KVVLPNGDVV KTASRARKSA AGYDLTRLII
GSEGTLGVIT EITLRLQKIP QHSVVAVCNF PTVKDAADVA IATMMSGIQV SRVELLDEVQ
IRAINMANGK NLTEAPTLMF EFIGTEAYTR EQTQIVQQIA SKHNGSDFMF AEEPEAKKEL
WKIRKEALWA CYAMAPGHEA MITDVCVPLS HLAELISRSK KELDASSLLC TVIAHAGDGN
FHTCIMFDPS SEEQRREAER LNHFMVHSAL SMDGTCTGEH GVGTGKMKYL EKELGIEALQ
TMKRIKKTLD PNDIMNPGKL IPPHVCF


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