DGOD_ECOLI
ID DGOD_ECOLI Reviewed; 382 AA.
AC Q6BF17; P31458; Q2M804;
DT 23-NOV-2004, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=D-galactonate dehydratase;
DE Short=GalD;
DE EC=4.2.1.6;
GN Name=dgoD; Synonyms=yidU; OrderedLocusNames=b4478, JW5629;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP SEQUENCE REVISION.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, PATHWAY, AND INDUCTION.
RC STRAIN=K12;
RX PubMed=324806; DOI=10.1016/0014-5793(77)80234-2;
RA Deacon J., Cooper R.A.;
RT "D-galactonate utilisation by enteric bacteria. The catabolic pathway in
RT Escherichia coli.";
RL FEBS Lett. 77:201-205(1977).
RN [6]
RP REPRESSION BY GLUCOSE, AND GENETIC LOCATION.
RC STRAIN=K12;
RX PubMed=211976; DOI=10.1007/bf00415730;
RA Cooper R.A.;
RT "The utilisation of D-galactonate and D-2-oxo-3-deoxygalactonate by
RT Escherichia coli K-12. Biochemical and genetical studies.";
RL Arch. Microbiol. 118:199-206(1978).
RN [7]
RP FUNCTION, KINETIC PARAMETERS, CATALYTIC MECHANISM, REACTION
RP STEREOCHEMISTRY, AND MUTAGENESIS OF HIS-185; HIS-285 AND GLU-310.
RA Wieczorek S.J., Kalivoda K.A., Clifton J.G., Ringe D., Petsko G.A.,
RA Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily:
RT identification of a 'new' general acid catalyst in the active site of D-
RT galactonate dehydratase from Escherichia coli.";
RL J. Am. Chem. Soc. 121:4540-4541(1999).
RN [8]
RP INDUCTION, OPERON, AND DISRUPTION PHENOTYPE.
RX PubMed=30455279; DOI=10.1128/jb.00281-18;
RA Singh B., Arya G., Kundu N., Sangwan A., Nongthombam S., Chaba R.;
RT "Molecular and functional insights into the regulation of D-galactonate
RT metabolism by the transcriptional regulator DgoR in Escherichia coli.";
RL J. Bacteriol. 201:e00281-e00281(2019).
CC -!- FUNCTION: Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-
CC D-galactonate. {ECO:0000269|PubMed:324806, ECO:0000269|Ref.7}.
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;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.5 mM for D-galactonate {ECO:0000269|Ref.7};
CC -!- PATHWAY: Carbohydrate acid metabolism; D-galactonate degradation; D-
CC glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 1/3.
CC {ECO:0000269|PubMed:324806}.
CC -!- INDUCTION: Part of the dgoRKADT operon, which encodes proteins for the
CC metabolism of D-galactonate (PubMed:30455279). Negatively regulated by
CC DgoR (PubMed:30455279). Induced by galactonate, but not by glycerol,
CC gluconate or galactose (PubMed:324806, PubMed:30455279). Repressed by
CC glucose (PubMed:211976). {ECO:0000269|PubMed:211976,
CC ECO:0000269|PubMed:30455279, ECO:0000269|PubMed:324806}.
CC -!- DISRUPTION PHENOTYPE: Deletion mutant cannot grow on D-galactonate.
CC {ECO:0000269|PubMed:30455279}.
CC -!- MISCELLANEOUS: Reaction proceeds via an anti dehydration.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA62044.1; Type=Frameshift; Note=The frameshift in position 1 caused the prediction of an ORF that fused dgoA and dgoD.; Evidence={ECO:0000305};
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DR EMBL; L10328; AAA62044.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00096; AAT48197.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77602.1; -; Genomic_DNA.
DR PIR; E65171; E65171.
DR RefSeq; WP_000705001.1; NZ_STEB01000015.1.
DR RefSeq; YP_026237.1; NC_000913.3.
DR AlphaFoldDB; Q6BF17; -.
DR SMR; Q6BF17; -.
DR STRING; 511145.b4478; -.
DR PaxDb; Q6BF17; -.
DR PRIDE; Q6BF17; -.
DR DNASU; 2847765; -.
DR EnsemblBacteria; AAT48197; AAT48197; b4478.
DR EnsemblBacteria; BAE77602; BAE77602; BAE77602.
DR GeneID; 2847765; -.
DR GeneID; 66672410; -.
DR KEGG; ecj:JW5629; -.
DR KEGG; eco:b4478; -.
DR PATRIC; fig|1411691.4.peg.3011; -.
DR EchoBASE; EB4309; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_3_2_6; -.
DR InParanoid; Q6BF17; -.
DR OMA; PRWCFLK; -.
DR PhylomeDB; Q6BF17; -.
DR BioCyc; EcoCyc:GALACTONATE-DEHYDRATASE-MON; -.
DR BioCyc; MetaCyc:GALACTONATE-DEHYDRATASE-MON; -.
DR BRENDA; 4.2.1.6; 2026.
DR UniPathway; UPA00081; UER00518.
DR PRO; PR:Q6BF17; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; 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:cellular amino acid catabolic process; IEA:InterPro.
DR GO; GO:0034194; P:D-galactonate catabolic process; IMP:EcoCyc.
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 Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..382
FT /note="D-galactonate dehydratase"
FT /id="PRO_0000171259"
FT ACT_SITE 185
FT /note="Proton donor"
FT ACT_SITE 285
FT /note="Proton acceptor"
FT BINDING 183
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 209
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 258
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000250"
FT SITE 310
FT /note="Transition state stabilizer"
FT MUTAGEN 185
FT /note="H->N,Q: Loss of activity."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 285
FT /note="H->N: Loss of activity."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 310
FT /note="E->Q: Loss of activity."
FT /evidence="ECO:0000269|Ref.7"
FT CONFLICT 137
FT /note="E -> Q (in Ref. 1; AAA62044)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 382 AA; 42523 MW; B38D4E0B95FD7041 CRC64;
MKITKITTYR LPPRWMFLKI ETDEGVVGWG EPVIEGRART VEAAVHELGD YLIGQDPSRI
NDLWQVMYRA GFYRGGPILM SAIAGIDQAL WDIKGKVLNA PVWQLMGGLV RDKIKAYSWV
GGDRPADVID GIKTLREIGF DTFKLNGCEE LGLIDNSRAV DAAVNTVAQI REAFGNQIEF
GLDFHGRVSA PMAKVLIKEL EPYRPLFIEE PVLAEQAEYY PKLAAQTHIP LAAGERMFSR
FDFKRVLEAG GISILQPDLS HAGGITECYK IAGMAEAYDV TLAPHCPLGP IALAACLHID
FVSYNAVLQE QSMGIHYNKG AELLDFVKNK EDFSMVGGFF KPLTKPGLGV EIDEAKVIEF
SKNAPDWRNP LWRHEDNSVA EW
