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D-lactate dehydrogenase (EC 1.1.1.28) (Respiratory D-lactate dehydrogenase)

 DLD_ECOLI               Reviewed;         571 AA.
P06149; Q2MAU6;
01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
25-OCT-2017, entry version 155.
RecName: Full=Quinone-dependent D-lactate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_02092, ECO:0000305};
EC=1.1.5.12 {ECO:0000255|HAMAP-Rule:MF_02092, ECO:0000269|PubMed:3013300, ECO:0000269|PubMed:7578233};
AltName: Full=(R)-lactate:quinone 2-oxidoreductase {ECO:0000305};
AltName: Full=D-lactate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_02092, ECO:0000303|PubMed:4575624, ECO:0000303|PubMed:4582730};
Short=D-LDH {ECO:0000255|HAMAP-Rule:MF_02092, ECO:0000303|PubMed:3882663};
AltName: Full=Respiratory D-lactate dehydrogenase {ECO:0000305};
Name=dld {ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000303|PubMed:6386470}; OrderedLocusNames=b2133, JW2121;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=6386470; DOI=10.1111/j.1432-1033.1984.tb08473.x;
Campbell H.D., Rogers B.L., Young I.G.;
"Nucleotide sequence of the respiratory D-lactate dehydrogenase gene
of Escherichia coli.";
Eur. J. Biochem. 144:367-373(1984).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-18.
PubMed=3882663;
Rule G.S., Pratt E.A., Chin C.C.Q., Wold F., Ho C.;
"Overproduction and nucleotide sequence of the respiratory D-lactate
dehydrogenase of Escherichia coli.";
J. Bacteriol. 161:1059-1068(1985).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / BHB2600;
Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
Church G.M.;
"Automated multiplex sequencing of the E.coli genome.";
Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[7]
FUNCTION, COFACTOR, AND SUBCELLULAR LOCATION.
PubMed=4575624;
Futai M.;
"Membrane D-lactate dehydrogenase from Escherichia coli. Purification
and properties.";
Biochemistry 12:2468-2474(1973).
[8]
FUNCTION, COFACTOR, ENZYME REGULATION, AND SUBCELLULAR LOCATION.
STRAIN=ML 308-225;
PubMed=4582730;
Kohn L.D., Kaback H.R.;
"Mechanisms of active transport in isolated bacterial membrane
vesicles. XV. Purification and properties of the membrane-bound D-
lactate dehydrogenase from Escherichia coli.";
J. Biol. Chem. 248:7012-7017(1973).
[9]
SUBCELLULAR LOCATION.
STRAIN=ML 308-225;
PubMed=1092688;
Short S.A., Kaback H.R., Kohn L.D.;
"Localization of D-lactate dehydrogenase in native and reconstituted
Escherichia coli membrane vesicles.";
J. Biol. Chem. 250:4291-4296(1975).
[10]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=3013300;
Matsushita K., Kaback H.R.;
"D-lactate oxidation and generation of the proton electrochemical
gradient in membrane vesicles from Escherichia coli GR19N and in
proteoliposomes reconstituted with purified D-lactate dehydrogenase
and cytochrome o oxidase.";
Biochemistry 25:2321-2327(1986).
[11]
FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=2185834;
Peersen O.B., Pratt E.A., Truong H.T., Ho C., Rule G.S.;
"Site-specific incorporation of 5-fluorotryptophan as a probe of the
structure and function of the membrane-bound D-lactate dehydrogenase
of Escherichia coli: a 19F nuclear magnetic resonance study.";
Biochemistry 29:3256-3262(1990).
[12]
FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
PubMed=7578233;
Sun Z.Y., Dowd S.R., Felix C., Hyde J.S., Ho C.;
"Stopped-flow kinetic and biophysical studies of membrane-associated
D-lactate dehydrogenase of Escherichia coli.";
Biochim. Biophys. Acta 1252:269-277(1995).
[13]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF MUTANT TRP-368 IN COMPLEX
WITH FAD, COFACTOR, SUBCELLULAR LOCATION, AND DOMAIN.
PubMed=10944213; DOI=10.1073/pnas.97.17.9413;
Dym O., Pratt E.A., Ho C., Eisenberg D.;
"The crystal structure of D-lactate dehydrogenase, a peripheral
membrane respiratory enzyme.";
Proc. Natl. Acad. Sci. U.S.A. 97:9413-9418(2000).
-!- FUNCTION: Catalyzes the oxidation of D-lactate to pyruvate.
Electrons derived from D-lactate oxidation are transferred to the
ubiquinone/cytochrome electron transfer chain, where they may be
used to provide energy for the active transport of a variety of
amino acids and sugars across the membrane.
{ECO:0000269|PubMed:2185834, ECO:0000269|PubMed:3013300,
ECO:0000269|PubMed:4575624, ECO:0000269|PubMed:4582730,
ECO:0000269|PubMed:7578233}.
-!- CATALYTIC ACTIVITY: (R)-lactate + a quinone = pyruvate + a quinol.
{ECO:0000255|HAMAP-Rule:MF_02092, ECO:0000269|PubMed:3013300,
ECO:0000269|PubMed:7578233}.
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000269|PubMed:10944213, ECO:0000269|PubMed:4575624,
ECO:0000269|PubMed:4582730, ECO:0000269|PubMed:7578233};
-!- ENZYME REGULATION: Inhibited by 2-hydroxy-3-butynoic acid, but not
by p-chloromercuribenzoate, n-ethylmaleimide, or 5,5'-dithiobis(2-
nitrobenzoic acid). {ECO:0000269|PubMed:4582730}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.16 mM for D-lactate {ECO:0000269|PubMed:2185834};
-!- SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000255|HAMAP-
Rule:MF_02092, ECO:0000269|PubMed:1092688,
ECO:0000269|PubMed:4575624, ECO:0000269|PubMed:4582730};
Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000269|PubMed:1092688}; Cytoplasmic side {ECO:0000255|HAMAP-
Rule:MF_02092, ECO:0000269|PubMed:1092688}. Note=May bind the
membrane through electrostatic rather than hydrophobic forces.
{ECO:0000305|PubMed:10944213}.
-!- DOMAIN: Contains 3 domains: the flavin adenine dinucleotide (FAD)-
binding domain, the cap domain and the membrane-binding domain.
{ECO:0000269|PubMed:10944213}.
-!- SIMILARITY: Belongs to the quinone-dependent D-lactate
dehydrogenase family. {ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAA60530.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
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EMBL; M10038; AAA23688.1; -; Genomic_DNA.
EMBL; X01067; CAA25531.1; -; Genomic_DNA.
EMBL; U00007; AAA60530.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC75194.1; -; Genomic_DNA.
EMBL; AP009048; BAE76610.1; -; Genomic_DNA.
PIR; A21893; DEECDL.
RefSeq; NP_416637.1; NC_000913.3.
RefSeq; WP_000097403.1; NZ_LN832404.1.
PDB; 1F0X; X-ray; 1.90 A; A/B=1-571.
PDBsum; 1F0X; -.
ProteinModelPortal; P06149; -.
SMR; P06149; -.
BioGrid; 4260452; 15.
IntAct; P06149; 17.
STRING; 316385.ECDH10B_2289; -.
BindingDB; P06149; -.
DrugBank; DB03147; Flavin adenine dinucleotide.
DrugBank; DB00756; Hexachlorophene.
PaxDb; P06149; -.
PRIDE; P06149; -.
EnsemblBacteria; AAC75194; AAC75194; b2133.
EnsemblBacteria; BAE76610; BAE76610; BAE76610.
GeneID; 946653; -.
KEGG; ecj:JW2121; -.
KEGG; eco:b2133; -.
PATRIC; fig|1411691.4.peg.110; -.
EchoBASE; EB0227; -.
EcoGene; EG10231; dld.
eggNOG; ENOG4105CXG; Bacteria.
eggNOG; COG0277; LUCA.
HOGENOM; HOG000122232; -.
InParanoid; P06149; -.
KO; K03777; -.
BioCyc; EcoCyc:DLACTDEHYDROGFAD-MONOMER; -.
BioCyc; MetaCyc:DLACTDEHYDROGFAD-MONOMER; -.
BRENDA; 1.1.1.28; 2026.
EvolutionaryTrace; P06149; -.
PRO; PR:P06149; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0031234; C:extrinsic component of cytoplasmic side of plasma membrane; IDA:EcoCyc.
GO; GO:0005887; C:integral component of plasma membrane; IEA:InterPro.
GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
GO; GO:0051990; F:(R)-2-hydroxyglutarate dehydrogenase activity; IBA:GO_Central.
GO; GO:0004458; F:D-lactate dehydrogenase (cytochrome) activity; IBA:GO_Central.
GO; GO:0009055; F:electron carrier activity; IDA:EcoCyc.
GO; GO:0071949; F:FAD binding; IBA:GO_Central.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:EcoCyc.
GO; GO:0051287; F:NAD binding; IEA:InterPro.
GO; GO:0016901; F:oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor; IDA:EcoCyc.
GO; GO:0048038; F:quinone binding; IEA:UniProtKB-KW.
GO; GO:0009060; P:aerobic respiration; IDA:EcoCyc.
GO; GO:0009061; P:anaerobic respiration; IDA:EcoCyc.
GO; GO:0019516; P:lactate oxidation; IDA:EcoCyc.
GO; GO:0022904; P:respiratory electron transport chain; IDA:EcoCyc.
GO; GO:0055085; P:transmembrane transport; IEA:InterPro.
Gene3D; 3.30.1370.20; -; 1.
Gene3D; 3.30.43.10; -; 1.
Gene3D; 3.30.465.10; -; 1.
Gene3D; 3.30.70.610; -; 2.
HAMAP; MF_02092; DLDH_Dld; 1.
InterPro; IPR016169; CO_DH_flavot_FAD-bd_sub2.
InterPro; IPR016172; D-lactate_DH_C-sub1.
InterPro; IPR016173; D-lactate_DH_C-sub2.
InterPro; IPR012256; D_lactate_DH.
InterPro; IPR016166; FAD-bd_2.
InterPro; IPR036318; FAD-bd_2-like_sf.
InterPro; IPR016167; FAD-bd_2_sub1.
InterPro; IPR016164; FAD-linked_Oxase-like_C.
InterPro; IPR015409; Lactate_DH_C.
InterPro; IPR006094; Oxid_FAD_bind_N.
Pfam; PF01565; FAD_binding_4; 1.
Pfam; PF09330; Lact-deh-memb; 1.
PIRSF; PIRSF000101; D-lactate_dh; 1.
SUPFAM; SSF55103; SSF55103; 1.
SUPFAM; SSF56176; SSF56176; 1.
PROSITE; PS51387; FAD_PCMH; 1.
1: Evidence at protein level;
3D-structure; Cell inner membrane; Cell membrane; Complete proteome;
Direct protein sequencing; FAD; Flavoprotein; Membrane;
Oxidoreductase; Quinone; Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:3882663}.
CHAIN 2 571 Quinone-dependent D-lactate
dehydrogenase.
/FTId=PRO_0000079928.
DOMAIN 42 213 FAD-binding PCMH-type.
{ECO:0000255|HAMAP-Rule:MF_02092}.
NP_BIND 76 80 FAD. {ECO:0000244|PDB:1F0X,
ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000269|PubMed:10944213}.
NP_BIND 84 85 FAD. {ECO:0000244|PDB:1F0X,
ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000269|PubMed:10944213}.
BINDING 143 143 FAD; via amide nitrogen.
{ECO:0000244|PDB:1F0X, ECO:0000255|HAMAP-
Rule:MF_02092,
ECO:0000269|PubMed:10944213}.
BINDING 150 150 FAD. {ECO:0000244|PDB:1F0X,
ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000269|PubMed:10944213}.
BINDING 160 160 FAD; via amide nitrogen.
{ECO:0000244|PDB:1F0X, ECO:0000255|HAMAP-
Rule:MF_02092,
ECO:0000269|PubMed:10944213}.
BINDING 262 262 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000244|PDB:1F0X,
ECO:0000255|HAMAP-Rule:MF_02092,
ECO:0000269|PubMed:10944213}.
HELIX 10 20 {ECO:0000244|PDB:1F0X}.
HELIX 22 24 {ECO:0000244|PDB:1F0X}.
HELIX 29 36 {ECO:0000244|PDB:1F0X}.
STRAND 39 41 {ECO:0000244|PDB:1F0X}.
STRAND 47 50 {ECO:0000244|PDB:1F0X}.
HELIX 55 67 {ECO:0000244|PDB:1F0X}.
STRAND 71 77 {ECO:0000244|PDB:1F0X}.
STRAND 81 83 {ECO:0000244|PDB:1F0X}.
STRAND 96 100 {ECO:0000244|PDB:1F0X}.
STRAND 107 110 {ECO:0000244|PDB:1F0X}.
TURN 111 114 {ECO:0000244|PDB:1F0X}.
STRAND 115 118 {ECO:0000244|PDB:1F0X}.
HELIX 124 131 {ECO:0000244|PDB:1F0X}.
HELIX 132 134 {ECO:0000244|PDB:1F0X}.
HELIX 143 147 {ECO:0000244|PDB:1F0X}.
HELIX 151 156 {ECO:0000244|PDB:1F0X}.
STRAND 174 179 {ECO:0000244|PDB:1F0X}.
STRAND 185 189 {ECO:0000244|PDB:1F0X}.
STRAND 191 193 {ECO:0000244|PDB:1F0X}.
HELIX 199 207 {ECO:0000244|PDB:1F0X}.
HELIX 213 215 {ECO:0000244|PDB:1F0X}.
HELIX 228 233 {ECO:0000244|PDB:1F0X}.
HELIX 247 249 {ECO:0000244|PDB:1F0X}.
STRAND 259 268 {ECO:0000244|PDB:1F0X}.
STRAND 277 284 {ECO:0000244|PDB:1F0X}.
HELIX 286 299 {ECO:0000244|PDB:1F0X}.
STRAND 305 311 {ECO:0000244|PDB:1F0X}.
HELIX 312 318 {ECO:0000244|PDB:1F0X}.
HELIX 379 387 {ECO:0000244|PDB:1F0X}.
STRAND 389 396 {ECO:0000244|PDB:1F0X}.
HELIX 400 414 {ECO:0000244|PDB:1F0X}.
STRAND 418 421 {ECO:0000244|PDB:1F0X}.
HELIX 424 434 {ECO:0000244|PDB:1F0X}.
HELIX 437 447 {ECO:0000244|PDB:1F0X}.
HELIX 449 451 {ECO:0000244|PDB:1F0X}.
STRAND 452 461 {ECO:0000244|PDB:1F0X}.
HELIX 475 478 {ECO:0000244|PDB:1F0X}.
STRAND 481 489 {ECO:0000244|PDB:1F0X}.
TURN 490 493 {ECO:0000244|PDB:1F0X}.
STRAND 494 502 {ECO:0000244|PDB:1F0X}.
HELIX 507 520 {ECO:0000244|PDB:1F0X}.
STRAND 527 529 {ECO:0000244|PDB:1F0X}.
TURN 532 534 {ECO:0000244|PDB:1F0X}.
HELIX 539 548 {ECO:0000244|PDB:1F0X}.
TURN 556 560 {ECO:0000244|PDB:1F0X}.
SEQUENCE 571 AA; 64612 MW; 77FB2C467CB4389F CRC64;
MSSMTTTDNK AFLNELARLV GSSHLLTDPA KTARYRKGFR SGQGDALAVV FPGSLLELWR
VLKACVTADK IILMQAANTG LTEGSTPNGN DYDRDVVIIS TLRLDKLHVL GKGEQVLAYP
GTTLYSLEKA LKPLGREPHS VIGSSCIGAS VIGGICNNSG GSLVQRGPAY TEMSLFARIN
EDGKLTLVNH LGIDLGETPE QILSKLDDDR IKDDDVRHDG RHAHDYDYVH RVRDIEADTP
ARYNADPDRL FESSGCAGKL AVFAVRLDTF EAEKNQQVFY IGTNQPEVLT EIRRHILANF
ENLPVAGEYM HRDIYDIAEK YGKDTFLMID KLGTDKMPFF FNLKGRTDAM LEKVKFFRPH
FTDRAMQKFG HLFPSHLPPR MKNWRDKYEH HLLLKMAGDG VGEAKSWLVD YFKQAEGDFF
VCTPEEGSKA FLHRFAAAGA AIRYQAVHSD EVEDILALDI ALRRNDTEWY EHLPPEIDSQ
LVHKLYYGHF MCYVFHQDYI VKKGVDVHAL KEQMLELLQQ RGAQYPAEHN VGHLYKAPET
LQKFYRENDP TNSMNPGIGK TSKRKNWQEV E


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