DGD_SALEP
ID DGD_SALEP Reviewed; 419 AA.
AC B5R541;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 04-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=D-galactonate dehydratase family member SEN1436;
DE EC=4.2.1.-;
DE AltName: Full=D-gluconate dehydratase;
DE EC=4.2.1.39;
GN OrderedLocusNames=SEN1436;
OS Salmonella enteritidis PT4 (strain P125109).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=550537;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=P125109;
RX PubMed=18583645; DOI=10.1101/gr.077404.108;
RA Thomson N.R., Clayton D.J., Windhorst D., Vernikos G., Davidson S.,
RA Churcher C., Quail M.A., Stevens M., Jones M.A., Watson M., Barron A.,
RA Layton A., Pickard D., Kingsley R.A., Bignell A., Clark L., Harris B.,
RA Ormond D., Abdellah Z., Brooks K., Cherevach I., Chillingworth T.,
RA Woodward J., Norberczak H., Lord A., Arrowsmith C., Jagels K., Moule S.,
RA Mungall K., Saunders M., Whitehead S., Chabalgoity J.A., Maskell D.,
RA Humphreys T., Roberts M., Barrow P.A., Dougan G., Parkhill J.;
RT "Comparative genome analysis of Salmonella enteritidis PT4 and Salmonella
RT gallinarum 287/91 provides insights into evolutionary and host adaptation
RT pathways.";
RL Genome Res. 18:1624-1637(2008).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND
RP GLUCONATE, FUNCTION, COFACTOR, CATALYTIC ACTIVITY, SUBUNIT, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=P125109;
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 0.04 sec(-1) with D-gluconate.
CC {ECO:0000269|PubMed:24697546};
CC -!- SUBUNIT: Homotetramer. {ECO:0000305|PubMed:24697546}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
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DR EMBL; AM933172; CAR33015.1; -; Genomic_DNA.
DR PDB; 3TW9; X-ray; 1.70 A; A/B/C/D=1-419.
DR PDB; 3TWA; X-ray; 1.80 A; A/B/C/D/E=1-419.
DR PDB; 3TWB; X-ray; 1.76 A; A/B/C/D/E=1-419.
DR PDBsum; 3TW9; -.
DR PDBsum; 3TWA; -.
DR PDBsum; 3TWB; -.
DR AlphaFoldDB; B5R541; -.
DR SMR; B5R541; -.
DR PRIDE; B5R541; -.
DR KEGG; set:SEN1436; -.
DR HOGENOM; CLU_030273_6_1_6; -.
DR OMA; IRCHVST; -.
DR Proteomes; UP000000613; 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 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 3D-structure; Lyase; Magnesium; Metal-binding.
FT CHAIN 1..419
FT /note="D-galactonate dehydratase family member SEN1436"
FT /id="PRO_0000429898"
FT ACT_SITE 160
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 227
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 45
FT /ligand="substrate"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 225
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 251
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 277
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 277
FT /ligand="substrate"
FT BINDING 298
FT /ligand="substrate"
FT BINDING 327
FT /ligand="substrate"
FT BINDING 331
FT /ligand="substrate"
FT BINDING 354
FT /ligand="substrate"
FT SITE 329
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"
FT STRAND 8..16
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 23..32
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 47..62
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:3TW9"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 87..108
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 112..115
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 120..129
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 135..148
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:3TWB"
FT HELIX 168..177
FT /evidence="ECO:0007829|PDB:3TW9"
FT TURN 178..180
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 198..216
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 218..225
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 232..242
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 248..251
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 256..261
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 262..268
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 282..290
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 301..304
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 307..319
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 330..332
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 334..346
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 360..365
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 371..373
FT /evidence="ECO:0007829|PDB:3TW9"
FT STRAND 376..378
FT /evidence="ECO:0007829|PDB:3TW9"
FT HELIX 391..394
FT /evidence="ECO:0007829|PDB:3TW9"
SQ SEQUENCE 419 AA; 46302 MW; 38F05894CB13BF9F CRC64;
MKVSNLKITN VKTILTAPGG IDLAVVKIET NEPGLYGLGC ATFTQRIFAV KSAIDEYMAP
FLVGKDPTRI EDIWQSGVVS GYWRNGPIMN NALSGVDMAL WDIKGKLAGM PVYDLLGGKC
RDGIPLYCHT DGGDEVEVED NIRARMEEGY QYVRCQMGMY GGAGTDDLKL IATQLARAKN
IQPKRSPRSK TPGIYFDPDA YAKSVPRLFD HLRNKLGFGI EFIHDVHERV TPVTAINLAK
TLEQYQLFYL EDPVAPENID WLKMLRQQSS TPISMGELFV NVNEWKPLID NRLIDYIRCH
VSTIGGITPA RKLAVYSELN GVRTAWHGPG DISPVGVCAN MHLDLSSPNF GIQEYTPMND
ALRDVFPGCP EIDHGYAYLN DKPGLGIDID EAKAAKYPCE GGIPSWTMAR TPDGTASRP
