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Entry: A0A086BNX2_9BIFI
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ID   A0A086BNX2_9BIFI        Unreviewed;       619 AA.
AC   A0A086BNX2;
DT   29-OCT-2014, integrated into UniProtKB/TrEMBL.
DT   29-OCT-2014, sequence version 1.
DT   24-JAN-2024, entry version 41.
DE   RecName: Full=Dihydroxy-acid dehydratase {ECO:0000256|ARBA:ARBA00029490, ECO:0000256|HAMAP-Rule:MF_00012};
DE            Short=DAD {ECO:0000256|HAMAP-Rule:MF_00012};
DE            EC=4.2.1.9 {ECO:0000256|ARBA:ARBA00029490, ECO:0000256|HAMAP-Rule:MF_00012};
GN   Name=ilvD {ECO:0000256|HAMAP-Rule:MF_00012};
GN   ORFNames=BBOMB_1502 {ECO:0000313|EMBL:KFF30636.1};
OS   Bifidobacterium bombi DSM 19703.
OC   Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales;
OC   Bifidobacteriaceae; Bifidobacterium.
OX   NCBI_TaxID=1341695 {ECO:0000313|EMBL:KFF30636.1, ECO:0000313|Proteomes:UP000028730};
RN   [1] {ECO:0000313|EMBL:KFF30636.1, ECO:0000313|Proteomes:UP000028730}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 19703 {ECO:0000313|EMBL:KFF30636.1,
RC   ECO:0000313|Proteomes:UP000028730};
RX   PubMed=25085493; DOI=10.1128/AEM.02308-14;
RA   Milani C., Lugli G.A., Duranti S., Turroni F., Bottacini F., Mangifesta M.,
RA   Sanchez B., Viappiani A., Mancabelli L., Taminiau B., Delcenserie V.,
RA   Barrangou R., Margolles A., van Sinderen D., Ventura M.;
RT   "Genomic encyclopedia of type strains of the genus Bifidobacterium.";
RL   Appl. Environ. Microbiol. 80:6290-6302(2014).
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:0000256|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;
CC         Evidence={ECO:0000256|ARBA:ARBA00029304};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24810;
CC         Evidence={ECO:0000256|ARBA:ARBA00029304};
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:0000256|HAMAP-Rule:MF_00012};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|ARBA:ARBA00001946,
CC         ECO:0000256|HAMAP-Rule:MF_00012};
CC   -!- COFACTOR:
CC       Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_00012};
CC       Note=Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis
CC       acid cofactor. {ECO:0000256|HAMAP-Rule:MF_00012};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; L-
CC       isoleucine from 2-oxobutanoate: step 3/4.
CC       {ECO:0000256|ARBA:ARBA00029437, ECO:0000256|HAMAP-Rule:MF_00012}.
CC   -!- PATHWAY: Amino-acid biosynthesis; L-valine biosynthesis; L-valine from
CC       pyruvate: step 3/4. {ECO:0000256|ARBA:ARBA00029436, ECO:0000256|HAMAP-
CC       Rule:MF_00012}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00012}.
CC   -!- SIMILARITY: Belongs to the IlvD/Edd family.
CC       {ECO:0000256|ARBA:ARBA00006486, ECO:0000256|HAMAP-Rule:MF_00012}.
CC   -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {ECO:0000256|HAMAP-Rule:MF_00012}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:KFF30636.1}.
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DR   EMBL; ATLK01000002; KFF30636.1; -; Genomic_DNA.
DR   RefSeq; WP_044087781.1; NZ_JDTS01000007.1.
DR   AlphaFoldDB; A0A086BNX2; -.
DR   STRING; 1341695.BBOMB_1502; -.
DR   eggNOG; COG0129; Bacteria.
DR   OrthoDB; 9807077at2; -.
DR   UniPathway; UPA00047; UER00057.
DR   UniPathway; UPA00049; UER00061.
DR   Proteomes; UP000028730; Unassembled WGS sequence.
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; IlvD/EDD C-terminal domain-like; 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   NCBIfam; TIGR00110; ilvD; 1.
DR   PANTHER; PTHR43661; D-XYLONATE DEHYDRATASE; 1.
DR   PANTHER; PTHR43661:SF3; D-XYLONATE DEHYDRATASE YAGF-RELATED; 1.
DR   Pfam; PF00920; ILVD_EDD; 1.
DR   SUPFAM; SSF143975; IlvD/EDD N-terminal domain-like; 1.
DR   SUPFAM; SSF52016; LeuD/IlvD-like; 1.
DR   PROSITE; PS00886; ILVD_EDD_1; 1.
DR   PROSITE; PS00887; ILVD_EDD_2; 1.
PE   3: Inferred from homology;
KW   2Fe-2S {ECO:0000256|ARBA:ARBA00022714, ECO:0000256|HAMAP-Rule:MF_00012};
KW   Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW   Rule:MF_00012};
KW   Branched-chain amino acid biosynthesis {ECO:0000256|ARBA:ARBA00023304,
KW   ECO:0000256|HAMAP-Rule:MF_00012};
KW   Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_00012};
KW   Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW   Rule:MF_00012};
KW   Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_00012};
KW   Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00012};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_00012}; Reference proteome {ECO:0000313|Proteomes:UP000028730}.
FT   ACT_SITE        518
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00012"
FT   BINDING         81
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00012"
FT   BINDING         123
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000256|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:0000256|HAMAP-Rule:MF_00012"
FT   BINDING         492
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00012"
FT   MOD_RES         124
FT                   /note="N6-carboxylysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00012"
SQ   SEQUENCE   619 AA;  66166 MW;  E56DC307F2D45AE1 CRC64;
     MQMRSHNIMT GRMFAGARAL YRAAGVAGDD LGRKPIVAIA NSFSEFVPGH VHLNKVGRVV
     SNAVKEAGGI PREFNTIAVD DGIAMGHTGM LYSLPSRDII ADAIEYSVNA HCADALICIS
     NCDKITPGML MAALRLNIPT IFVSGGPMEA GETTLSDGTT QTTDLIDVMY ASADDDVSDE
     DLLAYEKTVC PTCGSCAGMF TANSMNCLTE ALGLALPGNG TTLASHGYRR QLFERAGRMA
     VQLAHRYYDE DDESVLPRCI ATKHAFENAM TMDVAMGGST NTVLHILAAA QSADVDFTLD
     DIERISHTVP CICKASPSGD WEIPDVHRAG GICGILGELD RAGKLNQDVH SVDYPTLQAK
     LNDWDIMRSS CLPEAKELYR AAPGHITSPE PFTHETLSND LDTDRVNGAI HDIEHPAVTE
     GGLAILRGNL APDGCVVKTA GVPQNIWKFH GPARVVESQE QAVDVILGDK LKKGEALVIR
     YEGPKGGPGM QEMLYPTSFV KGKGIGKDVA LITDGRYSGG SSGLSIGHVA PEAANKGPIA
     LIRDGDIIDI DIPARSINVE LTDEQFEQRR RELEAGDGYV AHRDRKVSLA LKAYAAFARS
     ADKGATRDPD LINKLSGLA
//
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