ID A0A3E1RG10_9BURK Unreviewed; 613 AA.
AC A0A3E1RG10;
DT 16-JAN-2019, integrated into UniProtKB/TrEMBL.
DT 16-JAN-2019, sequence version 1.
DT 24-JAN-2024, entry version 18.
DE RecName: Full=Phosphogluconate dehydratase {ECO:0000256|HAMAP-Rule:MF_02094};
DE EC=4.2.1.12 {ECO:0000256|HAMAP-Rule:MF_02094};
GN Name=edd {ECO:0000256|HAMAP-Rule:MF_02094};
GN ORFNames=DIC66_05565 {ECO:0000313|EMBL:RFO98181.1};
OS Rhodoferax lacus.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Rhodoferax.
OX NCBI_TaxID=2184758 {ECO:0000313|EMBL:RFO98181.1, ECO:0000313|Proteomes:UP000260665};
RN [1] {ECO:0000313|EMBL:RFO98181.1, ECO:0000313|Proteomes:UP000260665}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IMCC26218 {ECO:0000313|EMBL:RFO98181.1,
RC ECO:0000313|Proteomes:UP000260665};
RA Park M.;
RT "Rhodoferax soyangensis sp.nov., isolated from an oligotrophic freshwater
RT lake.";
RL Submitted (MAY-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the dehydration of 6-phospho-D-gluconate to 2-
CC dehydro-3-deoxy-6-phospho-D-gluconate. {ECO:0000256|HAMAP-
CC Rule:MF_02094}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-
CC gluconate + H2O; Xref=Rhea:RHEA:17277, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:57569, ChEBI:CHEBI:58759; EC=4.2.1.12;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_02094};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_02094};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000256|HAMAP-Rule:MF_02094};
CC -!- PATHWAY: Carbohydrate metabolism; Entner-Doudoroff pathway.
CC {ECO:0000256|HAMAP-Rule:MF_02094}.
CC -!- SIMILARITY: Belongs to the IlvD/Edd family.
CC {ECO:0000256|ARBA:ARBA00006486, ECO:0000256|HAMAP-Rule:MF_02094}.
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:RFO98181.1}.
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DR EMBL; QFZK01000002; RFO98181.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A3E1RG10; -.
DR OrthoDB; 9807077at2; -.
DR UniPathway; UPA00226; -.
DR Proteomes; UP000260665; Unassembled WGS sequence.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004456; F:phosphogluconate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046177; P:D-gluconate catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009255; P:Entner-Doudoroff pathway through 6-phosphogluconate; IEA:UniProtKB-UniRule.
DR Gene3D; 3.50.30.80; IlvD/EDD C-terminal domain-like; 1.
DR HAMAP; MF_02094; Edd; 1.
DR InterPro; IPR004786; 6-phosphgluc_deHydtase.
DR InterPro; IPR042096; Dihydro-acid_dehy_C.
DR InterPro; IPR000581; DiOHA_6PGluconate_deHydtase.
DR InterPro; IPR020558; DiOHA_6PGluconate_deHydtase_CS.
DR InterPro; IPR037237; IlvD/EDD_N.
DR NCBIfam; TIGR01196; edd; 1.
DR PANTHER; PTHR43661; D-XYLONATE DEHYDRATASE; 1.
DR PANTHER; PTHR43661:SF1; PHOSPHOGLUCONATE DEHYDRATASE; 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 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_02094};
KW Carbohydrate metabolism {ECO:0000256|ARBA:ARBA00023277, ECO:0000256|HAMAP-
KW Rule:MF_02094};
KW Gluconate utilization {ECO:0000256|ARBA:ARBA00023064, ECO:0000256|HAMAP-
KW Rule:MF_02094}; Iron {ECO:0000256|HAMAP-Rule:MF_02094};
KW Iron-sulfur {ECO:0000256|HAMAP-Rule:MF_02094};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_02094};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_02094};
KW Reference proteome {ECO:0000313|Proteomes:UP000260665}.
FT BINDING 163
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
FT BINDING 230
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
SQ SEQUENCE 613 AA; 64444 MW; 2287D3F590185D73 CRC64;
MAAPQNSPAL HPAVVAVTRR IRERSAPTRS AYLALLDAMA QRRPGAERMG CANVAHAFAA
LPGADKFKVV AEKAPNIGII TAYNDLLSAH QPLQHYPDLI KAEARKHGAT AQVAGGVPAM
CDGVTQGFEG MELSLFSRDT IAMATAVGLS HDVFDCALML GVCDKIVPGL LIGALHFGHL
PTVFVPAGPM TSGLSNNDKS KVREKAAQGL VGREELLAAE SAAYHGPGTC TFYGTANSNQ
MLLEAMGLHV PGTAFINPGN SVREELTREA ARTVLGITKA KRFAPIGKVV DERCIVNAMV
ALLATGGSTN HLIHWVAVAR AAGIVIDWND FSALSDVVPL LTRVYPNGSA DVNQFQDAGG
PGFVIRELLD AGFMHADVLT VRSGGLREYC GVPAAQADGS LQWTDAGASK DEAVVRPALA
PFSASGGLKL LQGNLGRSVI KISAVPDDRH IIEAPCRVFD SQDALHVAFK AGELDRDVIC
VVRWQGPQAN GMPELHKLTP PLAVLQGKGF RVALVTDGRM SGASGKVPAA IHVSPEAAAG
GDLARVRDGD VIRLDANAET LQVLVDATEW AARPLATMPE ALRAANGVGM GRELFANMRR
NALAAEQGAC TWL
//
