DGD_STRBB
ID DGD_STRBB Reviewed; 411 AA.
AC D7BPX0;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=D-galactonate dehydratase family member SBI_01856;
DE EC=4.2.1.-;
DE AltName: Full=D-gluconate dehydratase;
DE EC=4.2.1.39;
GN OrderedLocusNames=SBI_01856;
OS Streptomyces bingchenggensis (strain BCW-1).
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=749414;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=BCW-1;
RX PubMed=20581206; DOI=10.1128/jb.00596-10;
RA Wang X.J., Yan Y.J., Zhang B., An J., Wang J.J., Tian J., Jiang L.,
RA Chen Y.H., Huang S.X., Yin M., Zhang J., Gao A.L., Liu C.X., Zhu Z.X.,
RA Xiang W.S.;
RT "Genome sequence of the milbemycin-producing bacterium Streptomyces
RT bingchenggensis.";
RL J. Bacteriol. 192:4526-4527(2010).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=BCW-1;
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 0.01 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; CP002047; ADI04977.1; -; Genomic_DNA.
DR RefSeq; WP_014174456.1; NC_016582.1.
DR AlphaFoldDB; D7BPX0; -.
DR SMR; D7BPX0; -.
DR STRING; 749414.SBI_01856; -.
DR EnsemblBacteria; ADI04977; ADI04977; SBI_01856.
DR KEGG; sbh:SBI_01856; -.
DR PATRIC; fig|749414.3.peg.1920; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_11; -.
DR OMA; DWDTRAY; -.
DR OrthoDB; 1825548at2; -.
DR Proteomes; UP000000377; Chromosome.
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 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; 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 SFLD; SFLDG00033; mannonate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Lyase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..411
FT /note="D-galactonate dehydratase family member SBI_01856"
FT /id="PRO_0000429900"
FT ACT_SITE 167
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 221
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 45
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 130
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 219
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 245
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 271
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 271
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 292
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 321
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 325
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 348
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 323
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 411 AA; 45273 MW; 0E04FBD4E1FB23C7 CRC64;
MSRPAHKTDT IVAVDVLVTS PGRNFVALKI TTEQGLVGWG DATLNGRELA VASYLRDHVA
PLLIGRDPAR IEDTWQYLYR GAYWRRGPVT MTSIGAVDLA LWDIKGKATG QPVYQLLGGA
VRDRILTYTH ASGWEIPQLL DAVDERREQG FLAVRAQSGI PGLATVYGVS SGEAGYEPAD
RGAAPAVEVW DTDSYLRHAP RVLAAVREHV GPELKLLHDA HHRLTPGQAA RLGRALEEVD
LYWLEDVTPA ENQEVLRHIR HHTTVPLAIG EVFNTVWECQ TLITEQLIDF VRTCVTHAGG
ISHLRRIAAL AEVWQVRLGP HGPSDVSPVA LAASLHVGLA TPNFAIQEYM GYEPVVHEVF
RHAWSYADGH LHPGDQPGLG VEVDEALAAR FPYEPAYLPI ARRRDGSMTD W
