ID C7CIV2_METED Unreviewed; 609 AA.
AC C7CIV2;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 24-JAN-2024, entry version 71.
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 ECO:0000313|EMBL:CAX24432.1};
GN ORFNames=METD_I2774 {ECO:0000313|EMBL:CAX24432.1};
OS Methylorubrum extorquens (strain DSM 6343 / CIP 106787 / DM4)
OS (Methylobacterium extorquens).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Methylobacteriaceae; Methylorubrum.
OX NCBI_TaxID=661410 {ECO:0000313|EMBL:CAX24432.1, ECO:0000313|Proteomes:UP000008070};
RN [1] {ECO:0000313|Proteomes:UP000008070}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 6343 / CIP 106787 / DM4
RC {ECO:0000313|Proteomes:UP000008070};
RX PubMed=19440302; DOI=10.1371/journal.pone.0005584;
RA Vuilleumier S., Chistoserdova L., Lee M.-C., Bringel F., Lajus A., Zhou Y.,
RA Gourion B., Barbe V., Chang J., Cruveiller S., Dossat C., Gillett W.,
RA Gruffaz C., Haugen E., Hourcade E., Levy R., Mangenot S., Muller E.,
RA Nadalig T., Pagni M., Penny C., Peyraud R., Robinson D.G., Roche D.,
RA Rouy Z., Saenampechek C., Salvignol G., Vallenet D., Wu Z., Marx C.J.,
RA Vorholt J.A., Olson M.V., Kaul R., Weissenbach J., Medigue C.,
RA Lidstrom M.E.;
RT "Methylobacterium genome sequences: a reference blueprint to investigate
RT microbial metabolism of C1 compounds from natural and industrial sources.";
RL PLoS ONE 4:E5584-E5584(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}.
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DR EMBL; FP103042; CAX24432.1; -; Genomic_DNA.
DR RefSeq; WP_015822574.1; NC_012988.1.
DR AlphaFoldDB; C7CIV2; -.
DR GeneID; 72989697; -.
DR KEGG; mdi:METDI2774; -.
DR HOGENOM; CLU_014271_1_2_5; -.
DR OMA; CANIAHV; -.
DR UniPathway; UPA00226; -.
DR Proteomes; UP000008070; Chromosome.
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 156
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
FT BINDING 223
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
SQ SEQUENCE 609 AA; 64931 MW; 679ABA3299F2EC3B CRC64;
MPELHPEVAA VTERVIARSR ASRRAYLDLI EREREAGVHR PMLACGNLAH GFAASGEDKP
AIIAGRAMNI GIVTAYNDML SAHQPYGRYP EQIKLFAREV GATAQVAGGT PAMCDGVTQG
QRGMELSLFS RDTIALSTAV ALSHGMFEGA ALLGICDKIV PGLIIGALRF GHLPMILVPA
GPMPSGLANK EKQRIRQLYA EGKVGRAELL ESESASYHGA GTCTFYGTAN SNQMMMDVMG
LHMPGASFIN PGTRLRQAVT RSAIHRLTEI GWNGNDYRPL GRCIDERAIV NAIVGLLATG
GSTNHAIHIP AMARAAGIVV DWEDFDRLSG VVPLIARVYP NGAGDVNHFH AAGGMSYVIA
SLIDAGLLHD DLLTVAGTRL RDHARDPKLL GEGNDLTFED APAEPLDEAM LRPPSRPFQP
DGGMRLVKGN LGRATFKTSA VDPERRTIEA PARVFSDQDE VIAAFKAGEL ERDVVVVVRF
QGPRANGMPE LHKLTPPLGV LQDRGHKVAL VTDGRMSGAS GKVPAAIHVS PEAVGGGPIS
RIRDGDIVRL SAEQRLLEVL VDSAEWDSRE DAVRPPDGLG TGRELFAFMR QGADDAERGG
SAMLAAAGL
//