ID A0A411WFJ7_9GAMM Unreviewed; 382 AA.
AC A0A411WFJ7;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 27-MAR-2024, entry version 18.
DE RecName: Full=D-galactonate dehydratase {ECO:0000256|HAMAP-Rule:MF_01289};
DE Short=GalD {ECO:0000256|HAMAP-Rule:MF_01289};
DE EC=4.2.1.6 {ECO:0000256|HAMAP-Rule:MF_01289};
GN Name=dgoD {ECO:0000256|HAMAP-Rule:MF_01289,
GN ECO:0000313|EMBL:QBH94973.1};
GN ORFNames=EKN56_00210 {ECO:0000313|EMBL:QBH94973.1};
OS Limnobaculum zhutongyuii.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Budviciaceae; Limnobaculum.
OX NCBI_TaxID=2498113 {ECO:0000313|EMBL:QBH94973.1, ECO:0000313|Proteomes:UP000293154};
RN [1] {ECO:0000313|EMBL:QBH94973.1, ECO:0000313|Proteomes:UP000293154}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CF-458 {ECO:0000313|EMBL:QBH94973.1,
RC ECO:0000313|Proteomes:UP000293154};
RA Ge Y.;
RT "Pragia sp. nov. isolated from the gut tract of Carduelis flavirostris.";
RL Submitted (MAR-2019) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-
CC D-galactonate. {ECO:0000256|HAMAP-Rule:MF_01289}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O;
CC Xref=Rhea:RHEA:18649, ChEBI:CHEBI:12931, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:57989; EC=4.2.1.6; Evidence={ECO:0000256|HAMAP-
CC Rule:MF_01289};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01289};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|HAMAP-Rule:MF_01289};
CC -!- PATHWAY: Carbohydrate acid metabolism; D-galactonate degradation; D-
CC glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 1/3.
CC {ECO:0000256|HAMAP-Rule:MF_01289}.
CC -!- MISCELLANEOUS: Reaction proceeds via an anti dehydration.
CC {ECO:0000256|HAMAP-Rule:MF_01289}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000256|HAMAP-Rule:MF_01289}.
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DR EMBL; CP034752; QBH94973.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A411WFJ7; -.
DR KEGG; prag:EKN56_00210; -.
DR OrthoDB; 103536at2; -.
DR UniPathway; UPA00081; UER00518.
DR Proteomes; UP000293154; Chromosome.
DR GO; GO:0008869; F:galactonate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009063; P:amino acid catabolic process; IEA:InterPro.
DR GO; GO:0034194; P:D-galactonate catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd03325; D-galactonate_dehydratase; 1.
DR Gene3D; 3.20.20.120; Enolase-like C-terminal domain; 1.
DR Gene3D; 3.30.390.10; Enolase-like, N-terminal domain; 1.
DR HAMAP; MF_01289; Galacton_dehydrat; 1.
DR InterPro; IPR034593; DgoD-like.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR023592; Galactonate_deHydtase.
DR InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR PANTHER; PTHR48080:SF2; D-GALACTONATE DEHYDRATASE; 1.
DR PANTHER; PTHR48080; D-GALACTONATE DEHYDRATASE-RELATED; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00003; D-galactonate_dehydratase; 1.
DR SFLD; SFLDG00179; mandelate_racemase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; Enolase C-terminal domain-like; 1.
DR SUPFAM; SSF54826; Enolase N-terminal domain-like; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 3: Inferred from homology;
KW Lyase {ECO:0000256|HAMAP-Rule:MF_01289, ECO:0000313|EMBL:QBH94973.1};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_01289};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01289}.
FT DOMAIN 125..230
FT /note="Mandelate racemase/muconate lactonizing enzyme C-
FT terminal"
FT /evidence="ECO:0000259|SMART:SM00922"
FT ACT_SITE 185
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
FT ACT_SITE 285
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
FT BINDING 183
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
FT BINDING 209
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
FT SITE 258
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
FT SITE 310
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01289"
SQ SEQUENCE 382 AA; 42473 MW; 6F57220DF2E940A5 CRC64;
MKITKLTTYR LAPRWMFLKV ETDEGVTGWG EPVIEGRARS VEAAVHELSE MIIGQDPARI
NDIWQTLYRG GFYRGGPILM SAISGIDQAL WDIKGKVLGV PVYQLLGGLV RDKIKAYSWV
GGDRPSDVIS GINKLKSIGF DTFKLNGCEE MGIIDNSRKV DEAVAVVAEI REAFGNSIEF
GLDFHGRVDA PMAKILIKEL EPYRPLFIEE PVLAEQAEYY VRLAAQTHIP IAAGERMFSR
FDFKRVLADG GLGIVQPDLS HAGGITECYK IAAMAESYDV AFAPHCPLGP IALASCLHID
FVARNAVLQE QSMGIHYNQG AELLDYVLNK EDFSMEDGHF YPPTKPGLGV EVNEELVIER
SKQAPDWRNP IWRYPDGAVA EW
//
