DGD_SALVI
ID DGD_SALVI Reviewed; 417 AA.
AC B5QBD4;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 04-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 44.
DE RecName: Full=D-galactonate dehydratase family member SeV_A0456;
DE EC=4.2.1.-;
DE AltName: Full=D-gluconate dehydratase;
DE EC=4.2.1.39;
GN ORFNames=SeV_A0456;
OS Salmonella virchow.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=48409;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SL491;
RX PubMed=21602358; DOI=10.1128/jb.00297-11;
RA Fricke W.F., Mammel M.K., McDermott P.F., Tartera C., White D.G.,
RA Leclerc J.E., Ravel J., Cebula T.A.;
RT "Comparative genomics of 28 Salmonella enterica isolates: evidence for
RT CRISPR-mediated adaptive sublineage evolution.";
RL J. Bacteriol. 193:3556-3568(2011).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=SL491;
RX PubMed=24697546; DOI=10.1021/bi500264p;
RA Wichelecki D.J., Balthazor B.M., Chau A.C., Vetting M.W., Fedorov A.A.,
RA Fedorov E.V., Lukk T., Patskovsky Y.V., Stead M.B., Hillerich B.S.,
RA Seidel R.D., Almo S.C., Gerlt J.A.;
RT "Discovery of function in the enolase superfamily: D-mannonate and D-
RT gluconate dehydratases in the D-mannonate dehydratase subgroup.";
RL Biochemistry 53:2722-2731(2014).
CC -!- FUNCTION: Has low D-gluconate dehydratase activity (in vitro),
CC suggesting that it has no significant role in D-gluconate degradation
CC in vivo. Has no detectable activity with a panel of 70 other acid
CC sugars (in vitro). {ECO:0000269|PubMed:24697546}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O;
CC Xref=Rhea:RHEA:21612, ChEBI:CHEBI:15377, ChEBI:CHEBI:18391,
CC ChEBI:CHEBI:57990; EC=4.2.1.39;
CC Evidence={ECO:0000269|PubMed:24697546};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:24697546};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:24697546};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 0.02 sec(-1) with D-gluconate.
CC {ECO:0000269|PubMed:24697546};
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
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DR EMBL; ABFH02000002; EDZ00842.1; -; Genomic_DNA.
DR RefSeq; WP_000067285.1; NZ_WFIR01000001.1.
DR AlphaFoldDB; B5QBD4; -.
DR SMR; B5QBD4; -.
DR GO; GO:0047929; F:gluconate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0016052; P:carbohydrate catabolic process; IDA:UniProtKB.
DR GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR034589; D-mannonate_dehydratase-like.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
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 PANTHER; PTHR48080:SF6; PTHR48080:SF6; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 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.
FT CHAIN 1..417
FT /note="D-galactonate dehydratase family member SeV_A0456"
FT /id="PRO_0000429899"
FT ACT_SITE 158
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 225
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 43
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 275
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 296
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 325
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 329
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 352
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 327
FT /note="Important for activity and substrate specificity;
FT Pro is observed in family members with low D-mannonate
FT dehydratase activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 417 AA; 46047 MW; 738E7D1A44066FEB CRC64;
MSNLKITNVK TILTAPGGID LAVVKIETNE PGLYGLGCAT FTQRIFAVKS AIDEYMAPFL
VGKDPTRIED IWQSGVVSGY WRNGPIMNNA LSGVDMALWD IKGKLAGMPV YDLLGGKCRD
GIPLYCHTDG GDEVEVEDNI RARMEEGYQY VRCQMGMYGG AGTDDLKLIA TQLARAKNIQ
PKRSPRSKTP GIYFDPDAYA KSVPRLFDHL RNKLGFGIEF IHDVHERVTP VTAINLAKTL
EQYQLFYLED PVAPENIDWL KMLRQQSSTP ISMGELFVNV NEWKPLIDNR LIDYIRCHVS
TIGGITPAKK LAVYSELNGV RTAWHGPGDI SPVGVCANMH LDLSSPNFGI QEYTPMNDAL
RDVFPGCPEI DHGYAYLNDK PGLGIDIDEA KAAKYPCEGG IPSWTMARTP DGTASRP
