ID D2YB67_VIBMI Unreviewed; 598 AA.
AC D2YB67;
DT 02-MAR-2010, integrated into UniProtKB/TrEMBL.
DT 02-MAR-2010, sequence version 1.
DT 24-JAN-2024, entry version 38.
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=VMB_07640 {ECO:0000313|EMBL:EEW08021.1};
OS Vibrio mimicus VM603.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=671074 {ECO:0000313|EMBL:EEW08021.1, ECO:0000313|Proteomes:UP000004827};
RN [1] {ECO:0000313|EMBL:EEW08021.1, ECO:0000313|Proteomes:UP000004827}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VM603 {ECO:0000313|EMBL:EEW08021.1,
RC ECO:0000313|Proteomes:UP000004827};
RX PubMed=19860885; DOI=10.1186/1471-2148-9-258;
RA Thompson C.C., Vicente A.C., Souza R.C., Vasconcelos A.T., Vesth T.,
RA Alves N.Jr., Ussery D.W., Iida T., Thompson F.L.;
RT "Genomic taxonomy of Vibrios.";
RL BMC Evol. Biol. 9:258-258(2009).
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:EEW08021.1}.
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DR EMBL; ACYU01000023; EEW08021.1; -; Genomic_DNA.
DR RefSeq; WP_000581777.1; NZ_ACYU01000023.1.
DR AlphaFoldDB; D2YB67; -.
DR UniPathway; UPA00226; -.
DR Proteomes; UP000004827; 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}.
FT BINDING 155
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
FT BINDING 222
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
SQ SEQUENCE 598 AA; 63714 MW; 15D101C414A85F3C CRC64;
MIHPVLAKVT QNLVERSREA RAAFIARSQA QEKAGKGRNS LSCGNLAHAV AASCSTEKKA
ILDFTRSNVA IVTSYNDMLS AHQPYQHYPD RIKSVLAEYG HTAQVAGGVP AMCDGVTQGQ
PGMDMSLFSR DLIAQATALS LSHNVFDATL LLGICDKIAP GQLMGALSYA HLPTAFMPAG
LMATGISNEE KVDIRQKYAA GEVGKDALLN MECQAYHAPG TCTFYGTANT NQLVFEAMGL
MLPGSAFVHP HSALRQALND AVTVKIASMT QGSAQYRPLY QVVTEQSLLN GIVALLASGG
STNHTIHMLA VARAAGILLT WQDISDLSDV VPLLAKVYPN GPADMNAFQQ AGGVPALMKR
LHEAKLLHAD VTPVFGEFSD QLSLPELVDG ELRWSPCEGT RDAQVIAASG ECFQTTGGTK
VLSGNLGRAV IKVSAVKDDQ RIIEAPAVVF LCQHEVEAAY QRGELNKDCI VVVTHNGPAA
NGMPELHKLM PILGNVQKAG FKVALVTDGR LSGASGKIPS AIHVSPEAVR GGAIGLVRDG
DLIRLDCSTG TLENRTDMSH RQALALDTER DQQMWGRELF KVMRQAVSSA EQGASFIV
//
