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ILVD_NITWN
ID   ILVD_NITWN              Reviewed;         614 AA.
AC   Q3SW60;
DT   07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2005, sequence version 1.
DT   03-AUG-2022, entry version 107.
DE   RecName: Full=Dihydroxy-acid dehydratase {ECO:0000255|HAMAP-Rule:MF_00012};
DE            Short=DAD {ECO:0000255|HAMAP-Rule:MF_00012};
DE            EC=4.2.1.9 {ECO:0000255|HAMAP-Rule:MF_00012};
GN   Name=ilvD {ECO:0000255|HAMAP-Rule:MF_00012}; OrderedLocusNames=Nwi_0213;
OS   Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 /
OS   NCIMB 11846 / Nb-255).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Nitrobacter.
OX   NCBI_TaxID=323098;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255;
RX   PubMed=16517654; DOI=10.1128/aem.72.3.2050-2063.2006;
RA   Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L.,
RA   Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J.,
RA   Hickey W.J.;
RT   "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium
RT   Nitrobacter winogradskyi Nb-255.";
RL   Appl. Environ. Microbiol. 72:2050-2063(2006).
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:0000255|HAMAP-Rule:MF_00012}.
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:0000255|HAMAP-
CC         Rule:MF_00012};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24810;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
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:0000255|HAMAP-Rule:MF_00012};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27695;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00012};
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   -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; L-
CC       isoleucine from 2-oxobutanoate: step 3/4. {ECO:0000255|HAMAP-
CC       Rule:MF_00012}.
CC   -!- PATHWAY: Amino-acid biosynthesis; L-valine biosynthesis; L-valine from
CC       pyruvate: step 3/4. {ECO:0000255|HAMAP-Rule:MF_00012}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00012}.
CC   -!- SIMILARITY: Belongs to the IlvD/Edd family. {ECO:0000255|HAMAP-
CC       Rule:MF_00012}.
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DR   EMBL; CP000115; ABA03481.1; -; Genomic_DNA.
DR   RefSeq; WP_011313548.1; NC_007406.1.
DR   AlphaFoldDB; Q3SW60; -.
DR   SMR; Q3SW60; -.
DR   STRING; 323098.Nwi_0213; -.
DR   EnsemblBacteria; ABA03481; ABA03481; Nwi_0213.
DR   KEGG; nwi:Nwi_0213; -.
DR   eggNOG; COG0129; Bacteria.
DR   HOGENOM; CLU_014271_4_3_5; -.
DR   OMA; TQGRNMA; -.
DR   OrthoDB; 193579at2; -.
DR   UniPathway; UPA00047; UER00057.
DR   UniPathway; UPA00049; UER00061.
DR   Proteomes; UP000002531; Chromosome.
DR   GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0004160; F:dihydroxy-acid dehydratase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0009097; P:isoleucine biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0009099; P:valine biosynthetic process; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   2Fe-2S; Amino-acid biosynthesis; Branched-chain amino acid biosynthesis;
KW   Iron; Iron-sulfur; Lyase; Magnesium; Metal-binding; Reference proteome.
FT   CHAIN           1..614
FT                   /note="Dihydroxy-acid dehydratase"
FT                   /id="PRO_0000225399"
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"
SQ   SEQUENCE   614 AA;  65467 MW;  B005A0938DDD4415 CRC64;
     MPAYRSRTST HGRNMAGARG LWRATGMKNE DFGKPIIAVV NSFTQFVPGH VHLKDLGQLV
     AREIEKAGGV AKEFHTIAVD DGIAMGHDGM LYSLPSREVI ADSVEYMVNA HCADAMVCIS
     NCDKITPGML MASLRLNIPS VFVSGGPMES GKVTLNGKVK SVDLIDAMVA AADDSVSDAD
     VEAIERSACP TCGSCSGMFT ANSMNCLTEA LGLALPGNGS VLATHADRKG LFVEAGHLIV
     DMARRYYEQN DERVLPRSVA SFKAFENAMT LDISMGGSTN TVLHLLAAAY EGEVPFTMAD
     IDRLSRRVPV LCKVAPSVAD VHLEDVHRAG GIMGILGELD RAGLIDASLP TVHSNSLREA
     LERWDIKRTK SESVRTFYTA APGGVRTEIA FSQDKRFEEL DADRAKGCIR DAEHAFSKDG
     GLAVLYGNIA RDGCIVKTAG VDDSILTFSG PARVFESQDA AVDAILGNRI KPGDVVLIRY
     EGPRGGPGMQ EMLYPTSYLK SKGLGKQCAL ITDGRFSGGS SGLSIGHVSP EAAEGGAIGL
     VEEGDLIAFD IPNRKVHLDV SDAELERRRA AMEAKGDKAW KPAAPRTRRI TMALKAYAAH
     TTSAALGAVR VVKD
 
 
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