DGOD_RALPJ
ID DGOD_RALPJ Reviewed; 382 AA.
AC B2UCA8;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=D-galactonate dehydratase {ECO:0000255|HAMAP-Rule:MF_01289};
DE Short=GalD {ECO:0000255|HAMAP-Rule:MF_01289};
DE EC=4.2.1.6 {ECO:0000255|HAMAP-Rule:MF_01289};
GN Name=dgoD {ECO:0000255|HAMAP-Rule:MF_01289}; OrderedLocusNames=Rpic_2990;
OS Ralstonia pickettii (strain 12J).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Ralstonia.
OX NCBI_TaxID=402626;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=12J;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Meincke L., Brettin T., Detter J.C.,
RA Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.,
RA Kyrpides N., Mikhailova N., Marsh T., Richardson P.;
RT "Complete sequence of chromosome 1 of Ralstonia pickettii 12J.";
RL Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-
CC D-galactonate. {ECO:0000255|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:0000255|HAMAP-
CC Rule:MF_01289};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01289};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|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:0000255|HAMAP-Rule:MF_01289}.
CC -!- MISCELLANEOUS: Reaction proceeds via an anti dehydration.
CC {ECO:0000255|HAMAP-Rule:MF_01289}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000255|HAMAP-Rule:MF_01289}.
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DR EMBL; CP001068; ACD28113.1; -; Genomic_DNA.
DR RefSeq; WP_012436402.1; NC_010682.1.
DR PDB; 3RR1; X-ray; 1.95 A; A/B=2-382.
DR PDB; 3RRA; X-ray; 2.30 A; A/B=2-382.
DR PDBsum; 3RR1; -.
DR PDBsum; 3RRA; -.
DR AlphaFoldDB; B2UCA8; -.
DR SMR; B2UCA8; -.
DR STRING; 402626.Rpic_2990; -.
DR EnsemblBacteria; ACD28113; ACD28113; Rpic_2990.
DR KEGG; rpi:Rpic_2990; -.
DR PATRIC; fig|402626.5.peg.4126; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_3_2_4; -.
DR OMA; PRWCFLK; -.
DR OrthoDB; 1825548at2; -.
DR UniPathway; UPA00081; UER00518.
DR EvolutionaryTrace; B2UCA8; -.
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:cellular 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; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR HAMAP; MF_01289; Galacton_dehydrat; 1.
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; IPR034593; Mandelate_racemase_DgoD-like.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR PANTHER; PTHR48080; PTHR48080; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00003; D-galactonate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding.
FT CHAIN 1..382
FT /note="D-galactonate dehydratase"
FT /id="PRO_1000140385"
FT ACT_SITE 185
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT ACT_SITE 285
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 183
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01289"
FT BINDING 209
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01289"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01289"
FT SITE 258
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01289"
FT SITE 310
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01289"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:3RR1"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 15..22
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 38..48
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:3RR1"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 60..69
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 77..98
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 102..105
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 125..137
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 142..147
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 157..172
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 175..177
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 190..200
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 218..224
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 240..249
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:3RR1"
FT TURN 259..263
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 264..276
FT /evidence="ECO:0007829|PDB:3RR1"
FT TURN 277..279
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 290..302
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 323..326
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 330..333
FT /evidence="ECO:0007829|PDB:3RR1"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:3RR1"
FT HELIX 354..362
FT /evidence="ECO:0007829|PDB:3RR1"
SQ SEQUENCE 382 AA; 42098 MW; 198F1A16BC5819F0 CRC64;
MKITRLTTYR LPPRWMFLKV ETDEGVTGWG EPVIEGRART VEAAVHELSD YLIGQDPSRI
NDLWQTMYRA GFYRGGPILM SAIAGIDQAL WDIKGKVLGV PVYELLGGLV RDKMRTYSWV
GGDRPADVIA GMKALQAGGF DHFKLNGCEE MGIIDTSRAV DAAVARVAEI RSAFGNTVEF
GLDFHGRVSA PMAKVLIKEL EPYRPLFIEE PVLAEQAETY ARLAAHTHLP IAAGERMFSR
FDFKRVLEAG GVSILQPDLS HAGGITECVK IAAMAEAYDV ALAPHCPLGP IALAACLHVD
FVSWNATLQE QSMGIHYNKG AELLDYVRNK ADFALEGGYI RPPRLPGLGV DIDEALVIER
SKEAPDWRNP VWRHADGSVA EW
