ID J2JGL5_9NOCA Unreviewed; 617 AA.
AC J2JGL5;
DT 03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 03-OCT-2012, sequence version 1.
DT 24-JAN-2024, entry version 35.
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:EJI99332.1};
GN ORFNames=JVH1_2940 {ECO:0000313|EMBL:EJI99332.1};
OS Rhodococcus sp. JVH1.
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae;
OC Rhodococcus.
OX NCBI_TaxID=745408 {ECO:0000313|EMBL:EJI99332.1, ECO:0000313|Proteomes:UP000009024};
RN [1] {ECO:0000313|EMBL:EJI99332.1, ECO:0000313|Proteomes:UP000009024}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JVH1 {ECO:0000313|EMBL:EJI99332.1,
RC ECO:0000313|Proteomes:UP000009024};
RX PubMed=22965106; DOI=10.1128/JB.01066-12;
RA Brooks S.L., Van Hamme J.D.;
RT "Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1.";
RL J. Bacteriol. 194:5492-5493(2012).
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:EJI99332.1}.
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DR EMBL; AKKP01000046; EJI99332.1; -; Genomic_DNA.
DR RefSeq; WP_009475031.1; NZ_AKKP01000046.1.
DR AlphaFoldDB; J2JGL5; -.
DR PATRIC; fig|745408.3.peg.2788; -.
DR UniPathway; UPA00226; -.
DR Proteomes; UP000009024; 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 164
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
FT BINDING 231
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
SQ SEQUENCE 617 AA; 64590 MW; 4064FB52CE35A449 CRC64;
MTDAPTPTAD VHPVLAAVTE RIIERSKPER TVYLNRIRAA GDRGPARGKL ACANLAHGFA
ASGPADKKAL RSFVKPNIAI VSSYNDMLSA HQPFEHFPRQ LKAAVMEAGG IAQFAGGVPA
MCDGITQGRD GMQLSLFSRD VIAMATAIGL SHDMFDGALM LGVCDKIVPG MLIGALGFGH
LPTIFVPAGP MTSGLPNNEK SRVRQLYAEG KAEREELLDA EAASYHGAGT CTFFGTANSN
QLLMEVMGLH LPGSSFVNPG TPLRDALTSE AGRRVTGLTA LGEEYTPVGE VVDEKAVVNG
CVALLATGGS TNHTMHLVAI ARAAGITLTW DDLSELSAVV PLLARIYPNG SADVNHFHAA
GGLGYVVSSM LDAGLLHEDV KTVVGPGLRR YTEEPKLSGE GVEWQPGTRI SLDTNVLRGP
EDPFDVNGGL KMLTGNLGSC VMKTSAVHPD HRVVTAPAKV FDDQLDFLAA FEAGTLTGDF
VAVLRYQGPR ANGMPELHKL TPVLGVLQDQ GRKVALVTDG RMSGASGKVP AAIHLTPEAA
ADGLLARVRD GDVLTVDAVT GSVNVHLDDE ELAARPATGR ALGADEWVGT GRELFAGLRA
AVGPATQGAS VFHPQPV
//
