ID I9WK27_9SPHN Unreviewed; 608 AA.
AC I9WK27;
DT 03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 03-OCT-2012, sequence version 1.
DT 24-JAN-2024, entry version 39.
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=WSK_0654 {ECO:0000313|EMBL:EIZ80681.1};
OS Novosphingobium sp. Rr 2-17.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=555793 {ECO:0000313|EMBL:EIZ80681.1, ECO:0000313|Proteomes:UP000004732};
RN [1] {ECO:0000313|EMBL:EIZ80681.1, ECO:0000313|Proteomes:UP000004732}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RR2-17 {ECO:0000313|Proteomes:UP000004732};
RX PubMed=22933764; DOI=10.1128/JB.01159-12;
RA Gan H.M., Chew T.H., Hudson A.O., Savka M.A.;
RT "Genome Sequence of Novosphingobium sp. Strain Rr 2-17, a Nopaline Crown
RT Gall-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.";
RL J. Bacteriol. 194:5137-5138(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:EIZ80681.1}.
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DR EMBL; AKFJ01000010; EIZ80681.1; -; Genomic_DNA.
DR RefSeq; WP_008993616.1; NZ_AKFJ01000010.1.
DR AlphaFoldDB; I9WK27; -.
DR PATRIC; fig|555793.3.peg.657; -.
DR eggNOG; COG0129; Bacteria.
DR OrthoDB; 9807077at2; -.
DR UniPathway; UPA00226; -.
DR Proteomes; UP000004732; 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:UP000004732}.
FT REGION 560..581
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 160
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
FT BINDING 227
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02094"
SQ SEQUENCE 608 AA; 64349 MW; 7E3501BC4F30C21A CRC64;
MANFHPGIHP VVARVTDRII QRSGESRKRY LDLVERETDR HSDRSFLSCS NLAHGFAASG
EDKPALSGSK AVNLGIVTAY NDMLSAHQPY GRYPEQMKLF AREVGATAQV ASGVPAMCDG
VTQGFDGMEL SLFSRDTIAL STAIALSHAM FDGMALLGIC DKIVPGLVIG ALRFGHLPAV
FVPAGPMPSG ISNKDKQKVR QLYAEGKVGR EELLASESAS YHAAGTCTFY GTANSNQMMM
EMMGLHVPGS AFVPPNTPLR QALTRKATHR LAEITRKGQD YRPMAHVVDE KAIVNAICGL
LATGGSTNHA IHLPAMARAA GVLINWEDFD ELSSVVPLIA RVYPNGSGDV NHFHAAGGMA
WIASELLGAG LAHGDVLTIA EGGMDAYATE PVLSGDTVEW RPAPKVSGDE TMLKPVSDPF
LPDGGMRLVE GNLGRATFKT SAVDAERWTI EAPCRVFDTQ EGVAQAFKAG ELDRDVVVVV
RFQGPRANGM PELHKLTPPL GVLQDRGHKV ALVTDGRMSG ASGKVPAAIH VTPEAFAGGP
LAFLQDGDIV RLSADDGTLS TTADLSGREP APTPPPASGM GRELFAMFRL NASGAEQGAS
SMLELAGL
//