DMGD_CHRSD
ID DMGD_CHRSD Reviewed; 403 AA.
AC Q1QT89;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=D-galactonate dehydratase family member ManD;
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 Name=manD; OrderedLocusNames=Csal_2974;
OS Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 /
OS NCIMB 13768 / 1H11).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales;
OC Halomonadaceae; Chromohalobacter.
OX NCBI_TaxID=290398;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11;
RX PubMed=22675587; DOI=10.4056/sigs.2285059;
RA Copeland A., O'Connor K., Lucas S., Lapidus A., Berry K.W., Detter J.C.,
RA Del Rio T.G., Hammon N., Dalin E., Tice H., Pitluck S., Bruce D.,
RA Goodwin L., Han C., Tapia R., Saunders E., Schmutz J., Brettin T.,
RA Larimer F., Land M., Hauser L., Vargas C., Nieto J.J., Kyrpides N.C.,
RA Ivanova N., Goker M., Klenk H.P., Csonka L.N., Woyke T.;
RT "Complete genome sequence of the halophilic and highly halotolerant
RT Chromohalobacter salexigens type strain (1H11(T)).";
RL Stand. Genomic Sci. 5:379-388(2011).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 2-403 IN COMPLEX WITH MAGNESIUM.
RA Fedorov A.A., Fedorov E.V., Wichelecki D., Gerlt J.A., Almo S.C.;
RT "Crystal structure of the mutant P317A of D-mannonate dehydratase from
RT Chromohalobacter salexigens complexed with Mg and D-Gluconate.";
RL Submitted (FEB-2011) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 2-403 IN COMPLEXES WITH
RP MAGNESIUM; D-MANNONATE AND 2-KETO-3-DEOXY-D-GLUCONATE, FUNCTION, CATALYTIC
RP ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF
RP HIS-313 AND PRO-315.
RC STRAIN=ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11;
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 0.02 sec(-1) with D-mannonate. kcat is 0.04 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; CP000285; ABE60319.1; -; Genomic_DNA.
DR RefSeq; WP_011508265.1; NC_007963.1.
DR PDB; 3BSM; X-ray; 2.20 A; A/B/C/D=2-403.
DR PDB; 3OW1; X-ray; 1.80 A; A/B/C/D/E/F/G/H=2-403.
DR PDB; 3P93; X-ray; 1.80 A; A/B/C/D/E/F/G/H=2-403.
DR PDB; 3PK7; X-ray; 1.64 A; A/B/C/D/E/F/G/H=2-403.
DR PDB; 3QKE; X-ray; 1.55 A; A/B/C/D/E/F/G/H=2-403.
DR PDB; 3RGT; X-ray; 1.90 A; A/B/C/D=2-403.
DR PDB; 4F4R; X-ray; 1.80 A; A=1-403.
DR PDB; 4K2S; X-ray; 1.70 A; A/B/C/D/E/F/G/H=2-403.
DR PDB; 4KPL; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-403.
DR PDB; 4KT2; X-ray; 1.80 A; A/B/C/D/E/F/G/H=1-403.
DR PDB; 4KWS; X-ray; 1.64 A; A/B/C/D/E/F/G/H=2-403.
DR PDBsum; 3BSM; -.
DR PDBsum; 3OW1; -.
DR PDBsum; 3P93; -.
DR PDBsum; 3PK7; -.
DR PDBsum; 3QKE; -.
DR PDBsum; 3RGT; -.
DR PDBsum; 4F4R; -.
DR PDBsum; 4K2S; -.
DR PDBsum; 4KPL; -.
DR PDBsum; 4KT2; -.
DR PDBsum; 4KWS; -.
DR AlphaFoldDB; Q1QT89; -.
DR SMR; Q1QT89; -.
DR STRING; 290398.Csal_2974; -.
DR EnsemblBacteria; ABE60319; ABE60319; Csal_2974.
DR KEGG; csa:Csal_2974; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_6; -.
DR OMA; EYMRHTE; -.
DR OrthoDB; 1825548at2; -.
DR EvolutionaryTrace; Q1QT89; -.
DR Proteomes; UP000000239; Chromosome.
DR GO; GO:0047929; F:gluconate dehydratase activity; IEA:UniProtKB-EC.
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 SFLD; SFLDG00033; mannonate_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.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..403
FT /note="D-galactonate dehydratase family member ManD"
FT /id="PRO_0000429881"
FT ACT_SITE 159
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 213
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 37
FT /ligand="substrate"
FT BINDING 122
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 211
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 237
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 263
FT /ligand="substrate"
FT BINDING 284
FT /ligand="substrate"
FT BINDING 313
FT /ligand="substrate"
FT BINDING 317
FT /ligand="substrate"
FT BINDING 340
FT /ligand="substrate"
FT SITE 315
FT /note="Important for activity and substrate specificity;
FT Pro is observed in family members with low D-mannonate
FT dehydratase activity"
FT MUTAGEN 163..170
FT /note="KTPGERYE->GAGGAGAG: Abolishes catalytic activity."
FT MUTAGEN 313
FT /note="H->N: Abolishes activity with D-gluconate and D-
FT mannonate."
FT /evidence="ECO:0000269|PubMed:24697546"
FT MUTAGEN 313
FT /note="H->Q: Abolishes activity with D-gluconate. No effect
FT on activity with D-mannonate."
FT /evidence="ECO:0000269|PubMed:24697546"
FT MUTAGEN 315
FT /note="P->A: Strongly increases activity with D-mannonate.
FT Slightly decreases activity with D-gluconate."
FT /evidence="ECO:0000269|PubMed:24697546"
FT STRAND 2..11
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 17..24
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 40..50
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:3QKE"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:3BSM"
FT HELIX 80..101
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 105..108
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 115..127
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 128..140
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 144..150
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 179..182
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 184..202
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 204..211
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 218..228
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 234..237
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 245..248
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 249..254
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 272..276
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 281..283
FT /evidence="ECO:0007829|PDB:3QKE"
FT TURN 287..291
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 292..304
FT /evidence="ECO:0007829|PDB:3QKE"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 309..312
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 320..332
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 336..340
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 346..351
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 368..373
FT /evidence="ECO:0007829|PDB:3QKE"
FT HELIX 377..380
FT /evidence="ECO:0007829|PDB:3QKE"
FT STRAND 392..395
FT /evidence="ECO:0007829|PDB:3QKE"
SQ SEQUENCE 403 AA; 45207 MW; 21717195BC4284E9 CRC64;
MKIRDAYTIV TCPGRNFVTL KIVTESGTHG IGDATLNGRE MAVAAYLDEH VVPALIGRDA
GRIEDTWQYL YRGAYWRRGP VTMTAIAAVD MALWDIKAKA AGMPLYQLLG GKSRERVMTY
AHCTGQTIED CLGEVARHVE LGYRAVRVQS GVPGIETTYG VAKTPGERYE PADSSLPAEH
VWSTEKYLNH APKLFAAVRE RFGDDLHVLH DVHHRLTPIE AARLGKAVEP YHLFWLEDCV
PAENQESLRL IREHTTTPLA IGEVFNSIHD CRELIQNQWI DYIRMPLTHG GGITAMRRVA
DLASLYHVRT GFHGPTDLSP VCLGAAIHFD TWVPNFGIQE HMPHTDETDA VFPHDYRFED
GHFLAGESPG HGVDIDEELA AKYPYERASL PVNRLEDGTL WHW
