DLD_ARATH
ID DLD_ARATH Reviewed; 567 AA.
AC Q94AX4; Q9FG12;
DT 20-APR-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=D-lactate dehydrogenase [cytochrome], mitochondrial {ECO:0000303|PubMed:19586914};
DE Short=AtD-LDH {ECO:0000303|PubMed:19586914};
DE EC=1.1.2.4 {ECO:0000269|PubMed:14966218, ECO:0000269|PubMed:19586914};
DE AltName: Full=D-lactate ferricytochrome C oxidoreductase {ECO:0000303|PubMed:19586914};
DE AltName: Full=Glycolate dehydrogenase {ECO:0000303|PubMed:14966218};
DE Flags: Precursor;
GN Name=DLD {ECO:0000303|PubMed:19586914};
GN Synonyms=GDH {ECO:0000303|PubMed:14966218};
GN OrderedLocusNames=At5g06580 {ECO:0000312|Araport:AT5G06580};
GN ORFNames=F15M7.11 {ECO:0000312|EMBL:BAB11407.1};
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;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases.
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].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, TISSUE SPECIFICITY,
RP INDUCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=14966218; DOI=10.1093/jxb/erh079;
RA Bari R., Kebeish R., Kalamajka R., Rademacher T., Peterhansel C.;
RT "A glycolate dehydrogenase in the mitochondria of Arabidopsis thaliana.";
RL J. Exp. Bot. 55:623-630(2004).
RN [5]
RP FUNCTION, SUBUNIT, COFACTOR, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19586914; DOI=10.1074/jbc.m109.021253;
RA Engqvist M., Drincovich M.F., Fluegge U.I., Maurino V.G.;
RT "Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic
RT capacities to participate in the last reactions of the methylglyoxal and
RT beta-oxidation pathways.";
RL J. Biol. Chem. 284:25026-25037(2009).
CC -!- FUNCTION: Catalyzes the stereospecific oxidation of D-lactate to
CC pyruvate. Involved in the detoxification of methylglyoxal and D-
CC lactate, but probably not involved in the metabolization of glycolate.
CC {ECO:0000269|PubMed:14966218, ECO:0000269|PubMed:19586914}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome
CC c] + 2 H(+) + pyruvate; Xref=Rhea:RHEA:13521, Rhea:RHEA-COMP:10350,
CC Rhea:RHEA-COMP:14399, ChEBI:CHEBI:15361, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16004, ChEBI:CHEBI:29033, ChEBI:CHEBI:29034; EC=1.1.2.4;
CC Evidence={ECO:0000269|PubMed:14966218, ECO:0000269|PubMed:19586914};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:19586914};
CC Note=Binds 1 FAD per monomer. {ECO:0000269|PubMed:19586914};
CC -!- ACTIVITY REGULATION: Inhibited by cyanide ions.
CC {ECO:0000269|PubMed:14966218}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=61 uM for D-2-hydroxybutyrate (with cytochrome c as acceptor
CC molecule) {ECO:0000269|PubMed:19586914};
CC KM=164 uM for D-lactate (with cytochrome c as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC KM=4486 uM for L-lactate (with cytochrome c as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC KM=8871 uM for D-glycerate (with cytochrome c as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC KM=432 uM for glycolate (with cytochrome c as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC KM=317 uM for D-lactate (with DCIP as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC KM=7134 uM for L-lactate (with DCIP as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC KM=596 uM for glycolate (with DCIP as acceptor molecule)
CC {ECO:0000269|PubMed:19586914};
CC Note=kcat is 88 min(-1) with D-2-hydroxybutyrate as substrate (with
CC cytochrome c as acceptor molecule) (PubMed:19586914). kcat is 65
CC min(-1) with D-lactate as substrate (with cytochrome c as acceptor
CC molecule) (PubMed:19586914). kcat is 7 min(-1) with L-lactate as
CC substrate (with cytochrome c as acceptor molecule) (PubMed:19586914).
CC kcat is 6 min(-1) with D-glycerate as substrate (with cytochrome c as
CC acceptor molecule) (PubMed:19586914). kcat is 0.1 min(-1) with
CC glycolate as substrate (with cytochrome c as acceptor molecule)
CC (PubMed:19586914). kcat is 73 min(-1) with D-lactate as substrate
CC (with DCIP as acceptor molecule) (PubMed:19586914). kcat is 5 min(-1)
CC with L-lactate as substrate (with DCIP as acceptor molecule)
CC (PubMed:19586914). kcat is 0.4 min(-1) with glycolate as substrate
CC (with DCIP as acceptor molecule) (PubMed:19586914).
CC {ECO:0000269|PubMed:19586914};
CC pH dependence:
CC Optimum pH is 8-9. {ECO:0000269|PubMed:19586914};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19586914}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14966218}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, stems, flowers and roots.
CC {ECO:0000269|PubMed:14966218}.
CC -!- INDUCTION: By light. {ECO:0000269|PubMed:14966218}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype when grown under standard
CC conditions, but developmental retardation and lethality when grown in
CC presence of methylglyoxal or D-lactate. {ECO:0000269|PubMed:19586914}.
CC -!- SIMILARITY: Belongs to the FAD-binding oxidoreductase/transferase type
CC 4 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB11407.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP002543; BAB11407.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91037.1; -; Genomic_DNA.
DR EMBL; AY045641; AAK73999.1; -; mRNA.
DR RefSeq; NP_568170.1; NM_120741.3.
DR AlphaFoldDB; Q94AX4; -.
DR STRING; 3702.AT5G06580.1; -.
DR SwissPalm; Q94AX4; -.
DR PaxDb; Q94AX4; -.
DR PRIDE; Q94AX4; -.
DR ProteomicsDB; 224168; -.
DR EnsemblPlants; AT5G06580.1; AT5G06580.1; AT5G06580.
DR GeneID; 830546; -.
DR Gramene; AT5G06580.1; AT5G06580.1; AT5G06580.
DR KEGG; ath:AT5G06580; -.
DR Araport; AT5G06580; -.
DR TAIR; locus:2144093; AT5G06580.
DR eggNOG; KOG1231; Eukaryota.
DR HOGENOM; CLU_017779_3_3_1; -.
DR InParanoid; Q94AX4; -.
DR OMA; TPRTCGE; -.
DR OrthoDB; 824020at2759; -.
DR PhylomeDB; Q94AX4; -.
DR BioCyc; ARA:AT5G06580-MON; -.
DR BioCyc; MetaCyc:AT5G06580-MON; -.
DR PRO; PR:Q94AX4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94AX4; baseline and differential.
DR Genevisible; Q94AX4; AT.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; HDA:TAIR.
DR GO; GO:0004458; F:D-lactate dehydrogenase (cytochrome) activity; IDA:TAIR.
DR GO; GO:0008720; F:D-lactate dehydrogenase activity; IMP:TAIR.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:UniProtKB.
DR GO; GO:0019154; F:glycolate dehydrogenase activity; IDA:TAIR.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:1903457; P:lactate catabolic process; IBA:GO_Central.
DR GO; GO:0051596; P:methylglyoxal catabolic process; IMP:UniProtKB.
DR Gene3D; 1.10.45.10; -; 1.
DR Gene3D; 3.30.465.10; -; 1.
DR InterPro; IPR016166; FAD-bd_PCMH.
DR InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR InterPro; IPR016164; FAD-linked_Oxase-like_C.
DR InterPro; IPR004113; FAD-linked_oxidase_C.
DR InterPro; IPR006094; Oxid_FAD_bind_N.
DR InterPro; IPR016171; Vanillyl_alc_oxidase_C-sub2.
DR Pfam; PF02913; FAD-oxidase_C; 1.
DR Pfam; PF01565; FAD_binding_4; 1.
DR SUPFAM; SSF55103; SSF55103; 1.
DR SUPFAM; SSF56176; SSF56176; 1.
DR PROSITE; PS51387; FAD_PCMH; 1.
PE 1: Evidence at protein level;
KW FAD; Flavoprotein; Mitochondrion; Oxidoreductase; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..56
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 57..567
FT /note="D-lactate dehydrogenase [cytochrome], mitochondrial"
FT /id="PRO_0000393388"
FT DOMAIN 142..319
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00718"
SQ 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
