DMGD_MUSP7
ID DMGD_MUSP7 Reviewed; 417 AA.
AC C6CBG9;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-SEP-2009, sequence version 1.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=D-galactonate dehydratase family member Dd703_0947;
DE EC=4.2.1.-;
DE AltName: Full=D-gluconate dehydratase;
DE EC=4.2.1.39;
DE AltName: Full=D-mannonate dehydratase;
DE EC=4.2.1.8;
GN OrderedLocusNames=Dd703_0947;
OS Musicola paradisiaca (strain Ech703) (Dickeya paradisiaca) (Dickeya
OS dadantii).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Pectobacteriaceae; Musicola.
OX NCBI_TaxID=579405;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ech703;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C.,
RA Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.,
RA Balakrishnan V., Glasner J., Perna N.T.;
RT "Complete sequence of Dickeya dadantii Ech703.";
RL Submitted (JUN-2009) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
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 dehydratase activity with D-mannonate and D-
CC gluconate, suggesting that these are not physiological substrates and
CC that it has no significant role in the in vivo degradation of these
CC compounds. 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-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O;
CC Xref=Rhea:RHEA:20097, ChEBI:CHEBI:15377, ChEBI:CHEBI:17767,
CC ChEBI:CHEBI:57990; EC=4.2.1.8;
CC Evidence={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-mannonate. kcat is 0.03 sec(-1) with
CC D-gluconate. {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; CP001654; ACS84754.1; -; Genomic_DNA.
DR RefSeq; WP_012764572.1; NC_012880.1.
DR PDB; 4IHC; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-417.
DR PDBsum; 4IHC; -.
DR AlphaFoldDB; C6CBG9; -.
DR SMR; C6CBG9; -.
DR STRING; 579405.Dd703_0947; -.
DR EnsemblBacteria; ACS84754; ACS84754; Dd703_0947.
DR KEGG; dda:Dd703_0947; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_6; -.
DR OMA; IRCHVST; -.
DR Proteomes; UP000002734; Chromosome.
DR GO; GO:0047929; F:gluconate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0008927; F:mannonate dehydratase activity; 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..417
FT /note="D-galactonate dehydratase family member Dd703_0947"
FT /id="PRO_0000429883"
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 127
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
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"
FT STRAND 6..14
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 21..30
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 45..54
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 56..60
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 68..76
FT /evidence="ECO:0007829|PDB:4IHC"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 85..106
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 110..113
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 118..132
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 133..145
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 150..157
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 196..214
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 216..223
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 230..240
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 241..243
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 254..259
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 260..266
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 271..273
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 280..288
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 299..302
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 305..317
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 328..330
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 332..344
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 358..363
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 369..371
FT /evidence="ECO:0007829|PDB:4IHC"
FT STRAND 374..376
FT /evidence="ECO:0007829|PDB:4IHC"
FT HELIX 389..392
FT /evidence="ECO:0007829|PDB:4IHC"
SQ SEQUENCE 417 AA; 46153 MW; 4FF2BB5D58CFEB69 CRC64;
MSKLKITNVK TILTAPGGID LAVVKVETNE PGLYGLGCAT FTQRIFAVKS AIDEYMAPFL
IGKDPTRIED IWQSAAVSGY WRNGPIMNNA LSGVDMALWD IKGKLAGMPV YELLGGKCRD
GIPLYCHTDG GDEVEVEDNI RARMEEGYQY VRCQMGMYGG AGTDDLKLIA TQLARAKNIQ
PKRSPRSKTP GIYFDPEAYA KSVPRLFEHL RNKLGFGIEF IHDVHERVTP VTAIQLAKTL
EPYQLFYLED PVAPENIDWL RMLRQQSSTP ISMGELFVNI NEWKPLIDNK LIDYIRCHVS
TIGGITPAKK LAVYSELNGV RTAWHGPGDI SPVGVCANMH LDMSSPNFGI QEYTPMNDAL
REVFPGCPEI DQGYAYVNDK PGLGIDINET LAEKYPCDGG IPSWTMARTP DGTASRP
