ILVD_ECOLI
ID ILVD_ECOLI Reviewed; 616 AA.
AC P05791; Q2M880;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 5.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=Dihydroxy-acid dehydratase {ECO:0000303|PubMed:7771772, ECO:0000303|PubMed:8325851};
DE Short=DAD {ECO:0000303|PubMed:7771772};
DE EC=4.2.1.9 {ECO:0000269|PubMed:13727223, ECO:0000269|PubMed:8325851};
GN Name=ilvD {ECO:0000255|HAMAP-Rule:MF_00012};
GN OrderedLocusNames=b3771, JW5605;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3315862; DOI=10.1016/0378-1119(87)90136-3;
RA Cox J.L., Cox B.J., Fidanza V., Calhoun D.H.;
RT "The complete nucleotide sequence of the ilvGMEDA cluster of Escherichia
RT coli K-12.";
RL Gene 56:185-198(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PATHWAY.
RC STRAIN=K12;
RX PubMed=3550695; DOI=10.1093/nar/15.5.2137;
RA Lawther R.P., Wek R.C., Lopes J.M., Pereira R., Taillon B.E.,
RA Hatfield G.W.;
RT "The complete nucleotide sequence of the ilvGMEDA operon of Escherichia
RT coli K-12.";
RL Nucleic Acids Res. 15:2137-2155(1987).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1379743; DOI=10.1126/science.1379743;
RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT 84.5 to 86.5 minutes.";
RL Science 257:771-778(1992).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP SEQUENCE REVISION.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-100.
RC STRAIN=K12;
RX PubMed=3897211; DOI=10.1093/oxfordjournals.jbchem.a135176;
RA Kuramitsu S., Ogawa T., Ogawa H., Kagamiyama H.;
RT "Branched-chain amino acid aminotransferase of Escherichia coli: nucleotide
RT sequence of the ilvE gene and the deduced amino acid sequence.";
RL J. Biochem. 97:993-999(1985).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 575-616.
RA Garrison E., Harms E.H., Umbarger H.E.;
RL Submitted (JUN-1987) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP PROTEIN SEQUENCE OF 2-23, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBUNIT.
RC STRAIN=K12 / JA221 / ATCC 33875 / DSM 5209;
RX PubMed=8325851; DOI=10.1016/s0021-9258(18)82394-8;
RA Flint D.H., Emptage M.H., Finnegan M.G., Fu W., Johnson M.K.;
RT "The role and properties of the iron-sulfur cluster in Escherichia coli
RT dihydroxy-acid dehydratase.";
RL J. Biol. Chem. 268:14732-14742(1993).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=13727223;
RA Myers J.W.;
RT "Dihydroxy acid dehydrase: an enzyme involved in the biosynthesis of
RT isoleucine and valine.";
RL J. Biol. Chem. 236:1414-1418(1961).
RN [11]
RP CATALYTIC ACTIVITY.
RX PubMed=7771772; DOI=10.1006/abbi.1995.1262;
RA Brown O.R., Smyk-Randall E., Draczynska-Lusiak B., Fee J.A.;
RT "Dihydroxy-acid dehydratase, a 4Fe-4S cluster-containing enzyme in
RT Escherichia coli: effects of intracellular superoxide dismutase on its
RT inactivation by oxidant stress.";
RL Arch. Biochem. Biophys. 319:10-22(1995).
CC -!- FUNCTION: Functions in the biosynthesis of branched-chain amino acids.
CC Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate
CC (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-
CC 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-
CC dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate),
CC the penultimate precursor to L-isoleucine and L-valine, respectively.
CC {ECO:0000269|PubMed:13727223, ECO:0000269|PubMed:8325851}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate
CC + H2O; Xref=Rhea:RHEA:24809, ChEBI:CHEBI:11851, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:49072; EC=4.2.1.9; Evidence={ECO:0000269|PubMed:13727223,
CC ECO:0000269|PubMed:7771772, ECO:0000269|PubMed:8325851};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24810;
CC Evidence={ECO:0000305|PubMed:13727223, ECO:0000305|PubMed:8325851};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-
CC oxopentanoate + H2O; Xref=Rhea:RHEA:27694, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:35146, ChEBI:CHEBI:49258; EC=4.2.1.9;
CC Evidence={ECO:0000269|PubMed:13727223};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27695;
CC Evidence={ECO:0000305|PubMed:13727223};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC Note=Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis
CC acid cofactor. {ECO:0000255|HAMAP-Rule:MF_00012};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.5 mM for racemic 2,3-dihydroxy-3-methylbutanoate
CC {ECO:0000269|PubMed:8325851};
CC KM=0.75 mM for (2R)-2,3-dihydroxy-3-methylbutanoate
CC {ECO:0000269|PubMed:8325851};
CC Note=Since only one of the isomers present in the racemic substrate
CC is active, the corrected Km would be 0.75 mM.
CC {ECO:0000269|PubMed:8325851};
CC pH dependence:
CC Optimum pH is 7.8-7.9. {ECO:0000269|PubMed:13727223};
CC -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; L-
CC isoleucine from 2-oxobutanoate: step 3/4. {ECO:0000255|HAMAP-
CC Rule:MF_00012, ECO:0000269|PubMed:3550695}.
CC -!- PATHWAY: Amino-acid biosynthesis; L-valine biosynthesis; L-valine from
CC pyruvate: step 3/4. {ECO:0000255|HAMAP-Rule:MF_00012,
CC ECO:0000269|PubMed:3550695}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:8325851}.
CC -!- SIMILARITY: Belongs to the IlvD/Edd family. {ECO:0000255|HAMAP-
CC Rule:MF_00012}.
CC -!- CAUTION: Was originally thought to contain a [4Fe-4S] cluster
CC (PubMed:7771772, PubMed:8325851). However, a more recent study in
CC M.tuberculosis has shown that this enzyme contains a [2Fe-2S] cluster,
CC which is unstable and subject to degradation.
CC {ECO:0000269|PubMed:7771772, ECO:0000269|PubMed:8325851, ECO:0000305}.
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DR EMBL; X04890; CAA28576.1; -; Genomic_DNA.
DR EMBL; M10313; AAB59053.1; -; Genomic_DNA.
DR EMBL; M87049; AAA67574.1; -; Genomic_DNA.
DR EMBL; U00096; AAT48208.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77526.1; -; Genomic_DNA.
DR EMBL; M32253; AAA24023.1; -; Genomic_DNA.
DR EMBL; X02413; CAA26263.1; -; Genomic_DNA.
DR EMBL; K03503; AAA24013.1; -; Genomic_DNA.
DR PIR; A27310; DWECDA.
DR RefSeq; WP_001127399.1; NZ_SSZK01000025.1.
DR RefSeq; YP_026248.1; NC_000913.3.
DR AlphaFoldDB; P05791; -.
DR SMR; P05791; -.
DR BioGRID; 4263329; 5.
DR DIP; DIP-10021N; -.
DR IntAct; P05791; 1.
DR STRING; 511145.b3771; -.
DR SWISS-2DPAGE; P05791; -.
DR jPOST; P05791; -.
DR PaxDb; P05791; -.
DR PRIDE; P05791; -.
DR EnsemblBacteria; AAT48208; AAT48208; b3771.
DR EnsemblBacteria; BAE77526; BAE77526; BAE77526.
DR GeneID; 948277; -.
DR KEGG; ecj:JW5605; -.
DR KEGG; eco:b3771; -.
DR PATRIC; fig|1411691.4.peg.2935; -.
DR EchoBASE; EB0491; -.
DR eggNOG; COG0129; Bacteria.
DR HOGENOM; CLU_014271_4_2_6; -.
DR InParanoid; P05791; -.
DR OMA; TQGRNMA; -.
DR PhylomeDB; P05791; -.
DR BioCyc; EcoCyc:DIHYDROXYACIDDEHYDRAT-MON; -.
DR BioCyc; MetaCyc:DIHYDROXYACIDDEHYDRAT-MON; -.
DR UniPathway; UPA00047; UER00057.
DR UniPathway; UPA00049; UER00061.
DR PRO; PR:P05791; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0004160; F:dihydroxy-acid dehydratase activity; IDA:EcoCyc.
DR GO; GO:0016836; F:hydro-lyase activity; IBA:GO_Central.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IDA:EcoCyc.
DR GO; GO:0009099; P:valine biosynthetic process; IDA:EcoCyc.
DR Gene3D; 3.50.30.80; -; 1.
DR HAMAP; MF_00012; IlvD; 1.
DR InterPro; IPR042096; Dihydro-acid_dehy_C.
DR InterPro; IPR004404; DihydroxyA_deHydtase.
DR InterPro; IPR000581; DiOHA_6PGluconate_deHydtase.
DR InterPro; IPR020558; DiOHA_6PGluconate_deHydtase_CS.
DR InterPro; IPR037237; IlvD/EDD_N.
DR Pfam; PF00920; ILVD_EDD; 1.
DR SUPFAM; SSF143975; SSF143975; 1.
DR TIGRFAMs; TIGR00110; ilvD; 1.
DR PROSITE; PS00886; ILVD_EDD_1; 1.
DR PROSITE; PS00887; ILVD_EDD_2; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; Amino-acid biosynthesis; Branched-chain amino acid biosynthesis;
KW Direct protein sequencing; Iron; Iron-sulfur; Lyase; Magnesium;
KW Metal-binding; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8325851"
FT CHAIN 2..616
FT /note="Dihydroxy-acid dehydratase"
FT /id="PRO_0000103465"
FT ACT_SITE 517
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 81
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 122
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 123
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 124
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 195
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 491
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT MOD_RES 124
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT CONFLICT 2..24
FT /note="PKYRSATTTHGRNMAGARALWRA -> VVIWRVLVRCGP (in Ref. 2;
FT AAA24023)"
FT /evidence="ECO:0000305"
FT CONFLICT 164
FT /note="L -> P (in Ref. 2; AAA24023)"
FT /evidence="ECO:0000305"
FT CONFLICT 408..437
FT /note="CIRSLEHAYSKDGGLAVLYGNFAENGCIVK -> VSARWNTPTAKTAAWRCS
FT TVILRKRLHRE (in Ref. 2; AAA24023)"
FT /evidence="ECO:0000305"
FT CONFLICT 610
FT /note="D -> H (in Ref. 2; AAA24023)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 616 AA; 65532 MW; 6F6DA053CFDA475B CRC64;
MPKYRSATTT HGRNMAGARA LWRATGMTDA DFGKPIIAVV NSFTQFVPGH VHLRDLGKLV
AEQIEAAGGV AKEFNTIAVD DGIAMGHGGM LYSLPSRELI ADSVEYMVNA HCADAMVCIS
NCDKITPGML MASLRLNIPV IFVSGGPMEA GKTKLSDQII KLDLVDAMIQ GADPKVSDSQ
SDQVERSACP TCGSCSGMFT ANSMNCLTEA LGLSQPGNGS LLATHADRKQ LFLNAGKRIV
ELTKRYYEQN DESALPRNIA SKAAFENAMT LDIAMGGSTN TVLHLLAAAQ EAEIDFTMSD
IDKLSRKVPQ LCKVAPSTQK YHMEDVHRAG GVIGILGELD RAGLLNRDVK NVLGLTLPQT
LEQYDVMLTQ DDAVKNMFRA GPAGIRTTQA FSQDCRWDTL DDDRANGCIR SLEHAYSKDG
GLAVLYGNFA ENGCIVKTAG VDDSILKFTG PAKVYESQDD AVEAILGGKV VAGDVVVIRY
EGPKGGPGMQ EMLYPTSFLK SMGLGKACAL ITDGRFSGGT SGLSIGHVSP EAASGGSIGL
IEDGDLIAID IPNRGIQLQV SDAELAARRE AQDARGDKAW TPKNRERQVS FALRAYASLA
TSADKGAVRD KSKLGG
