ILVD_PELPB
ID ILVD_PELPB Reviewed; 565 AA.
AC B4SDK2;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 73.
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=Ppha_2167;
OS Pelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1).
OC Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae;
OC Chlorobium/Pelodictyon group; Pelodictyon.
OX NCBI_TaxID=324925;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 5477 / BU-1;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Mikhailova N., Liu Z., Li T., Zhao F., Overmann J.,
RA Bryant D.A., Richardson P.;
RT "Complete sequence of Pelodictyon phaeoclathratiforme BU-1.";
RL Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases.
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; CP001110; ACF44370.1; -; Genomic_DNA.
DR RefSeq; WP_012508847.1; NC_011060.1.
DR AlphaFoldDB; B4SDK2; -.
DR SMR; B4SDK2; -.
DR STRING; 324925.Ppha_2167; -.
DR EnsemblBacteria; ACF44370; ACF44370; Ppha_2167.
DR KEGG; pph:Ppha_2167; -.
DR eggNOG; COG0129; Bacteria.
DR HOGENOM; CLU_014271_4_2_10; -.
DR OMA; TQGRNMA; -.
DR OrthoDB; 193579at2; -.
DR UniPathway; UPA00047; UER00057.
DR UniPathway; UPA00049; UER00061.
DR Proteomes; UP000002724; 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..565
FT /note="Dihydroxy-acid dehydratase"
FT /id="PRO_1000089397"
FT ACT_SITE 473
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 80
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 121
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 122
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 123
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 194
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT BINDING 447
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
FT MOD_RES 123
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00012"
SQ SEQUENCE 565 AA; 59705 MW; 2F4A26BA2B860D5E CRC64;
MRSDTIKTGF EKAPHRSLLK ATGSIVSNND FKKPFIGICN SYNELIPGHS HLQELGRIAK
EEVRKAGGVP FEFNTIGVCD GIAMGHIGMR YSLASRELIA DSVETVAQAH CLDGLVCIPN
CDKITPGMMM AALRINIPVI FVSGGPMKAG HTPSGQTVDL ISVFEAVGQF SAGKIGNEEL
ESIEESACPG CGSCSGMFTA NSMNCLSEAL GFALPGNGTI LAIDPRRNEL VREASRRIID
LVKKDIKPRD ILSRNALLNA FALDFAMGGS TNTILHTLAI ANEAELDFNF SELNALSAKT
PYICKVSPAT MAVHIEDVDR AGGVSAILHE LSRIDGLLDL STLTVTGKTL GENIADAEIL
DYTVIRSIDE PYSATGGLAV LFGNLAPQGA VVKTGAVAPE MMKHTGPAKI YDCQDDAIKG
IMGDDVKAGD VVVIRYEGPK GGPGMPEMLS PTSAIMGRGL GESVALITDG RFSGGSRGAC
IGHISPEAAE RGPIAALHNG DLITIDIPSR SISVNLTEET INERLAALKP FEPKIKKGYL
ARYAQMVTSA NTGAILKNPV SCEPK
