GUDD_ECOLI
ID GUDD_ECOLI Reviewed; 446 AA.
AC P0AES2; P76637; P78217; Q46914;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Glucarate dehydratase;
DE Short=GDH;
DE Short=GlucD;
DE EC=4.2.1.40 {ECO:0000269|PubMed:9772162};
DE AltName: Full=D-glucarate dehydratase {ECO:0000303|PubMed:11513584};
GN Name=gudD; Synonyms=ygcX; OrderedLocusNames=b2787, JW2758;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 315-446.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [4]
RP PROTEIN SEQUENCE OF 2-15, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC
RP ACTIVITY, AND FUNCTION.
RX PubMed=9772162; DOI=10.1021/bi981124f;
RA Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily:
RT characterization of the (D)-glucarate/galactarate catabolic pathway in
RT Escherichia coli.";
RL Biochemistry 37:14369-14375(1998).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND
RP MAGNESIUM IONS, MUTAGENESIS OF TYR-150; LYS-207; HIS-339 AND ASP-366,
RP COFACTOR, AND SUBUNIT.
RX PubMed=10769114; DOI=10.1021/bi992782i;
RA Gulick A.M., Hubbard B.K., Gerlt J.A., Rayment I.;
RT "Evolution of enzymatic activities in the enolase superfamily:
RT crystallographic and mutagenesis studies of the reaction catalyzed by D-
RT glucarate dehydratase from Escherichia coli.";
RL Biochemistry 39:4590-4602(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF MUTANT ASN-341 IN COMPLEX WITH
RP SUBSTRATE ANALOGS AND MAGNESIUM IONS, SUBUNIT, FUNCTION, MUTAGENESIS OF
RP ASN-341, AND ACTIVE SITE.
RX PubMed=11513584; DOI=10.1021/bi010733b;
RA Gulick A.M., Hubbard B.K., Gerlt J.A., Rayment I.;
RT "Evolution of enzymatic activities in the enolase superfamily:
RT identification of the general acid catalyst in the active site of D-
RT glucarate dehydratase from Escherichia coli.";
RL Biochemistry 40:10054-10062(2001).
CC -!- FUNCTION: Catalyzes the dehydration of glucarate or L-idarate to 5-
CC keto-4-deoxy-D-glucarate (5-kdGluc) (PubMed:9772162). Also catalyzes
CC the epimerization of D-glucarate and L-idarate (PubMed:11513584).
CC {ECO:0000269|PubMed:11513584, ECO:0000269|PubMed:9772162}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O;
CC Xref=Rhea:RHEA:14573, ChEBI:CHEBI:15377, ChEBI:CHEBI:30612,
CC ChEBI:CHEBI:42819; EC=4.2.1.40;
CC Evidence={ECO:0000269|PubMed:9772162};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:10769114};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=16 uM for idarate {ECO:0000269|PubMed:9772162};
CC KM=60 uM for glucarate {ECO:0000269|PubMed:9772162};
CC -!- PATHWAY: Carbohydrate acid metabolism; D-glucarate degradation; 2,5-
CC dioxopentanoate from D-glucarate: step 1/2.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10769114,
CC ECO:0000269|PubMed:11513584}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GlucD subfamily. {ECO:0000305}.
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DR EMBL; U00096; AAC75829.1; -; Genomic_DNA.
DR EMBL; U29581; AAB40437.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16572.2; -; Genomic_DNA.
DR PIR; G65060; G65060.
DR RefSeq; NP_417267.1; NC_000913.3.
DR RefSeq; WP_000098255.1; NZ_LN832404.1.
DR PDB; 1EC7; X-ray; 1.90 A; A/B/C/D=1-446.
DR PDB; 1EC8; X-ray; 1.90 A; A/B/C/D=1-446.
DR PDB; 1EC9; X-ray; 2.00 A; A/B/C/D=1-446.
DR PDB; 1ECQ; X-ray; 2.00 A; A/B/C/D=1-446.
DR PDB; 1JCT; X-ray; 2.75 A; A/B=1-446.
DR PDB; 1JDF; X-ray; 2.00 A; A/B/C/D=1-446.
DR PDB; 3PWG; X-ray; 2.00 A; A/B/C/D=1-446.
DR PDB; 3PWI; X-ray; 2.23 A; A/B=1-446.
DR PDB; 4GYP; X-ray; 2.10 A; A/B=1-446.
DR PDBsum; 1EC7; -.
DR PDBsum; 1EC8; -.
DR PDBsum; 1EC9; -.
DR PDBsum; 1ECQ; -.
DR PDBsum; 1JCT; -.
DR PDBsum; 1JDF; -.
DR PDBsum; 3PWG; -.
DR PDBsum; 3PWI; -.
DR PDBsum; 4GYP; -.
DR AlphaFoldDB; P0AES2; -.
DR SMR; P0AES2; -.
DR BioGRID; 4262287; 12.
DR IntAct; P0AES2; 3.
DR STRING; 511145.b2787; -.
DR DrugBank; DB03237; 2,3-Dihydroxy-5-Oxo-Hexanedioate.
DR DrugBank; DB03212; 4-Deoxyglucarate.
DR DrugBank; DB03603; Glucaric acid.
DR DrugBank; DB03734; Xylarohydroxamate.
DR jPOST; P0AES2; -.
DR PaxDb; P0AES2; -.
DR PRIDE; P0AES2; -.
DR EnsemblBacteria; AAC75829; AAC75829; b2787.
DR EnsemblBacteria; BAA16572; BAA16572; BAA16572.
DR GeneID; 947258; -.
DR KEGG; ecj:JW2758; -.
DR KEGG; eco:b2787; -.
DR PATRIC; fig|1411691.4.peg.3947; -.
DR EchoBASE; EB2959; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_9_0_6; -.
DR InParanoid; P0AES2; -.
DR OMA; MQYLIPN; -.
DR PhylomeDB; P0AES2; -.
DR BioCyc; EcoCyc:GLUCARDEHYDRA-MON; -.
DR BioCyc; MetaCyc:GLUCARDEHYDRA-MON; -.
DR BRENDA; 4.2.1.40; 2026.
DR SABIO-RK; P0AES2; -.
DR UniPathway; UPA00564; UER00627.
DR EvolutionaryTrace; P0AES2; -.
DR PRO; PR:P0AES2; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008872; F:glucarate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0042838; P:D-glucarate catabolic process; IDA:UniProtKB.
DR CDD; cd03323; D-glucarate_dehydratase; 1.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR017653; Glucarate_dehydratase.
DR InterPro; IPR034598; GlucD-like.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR034593; Mandelate_racemase_DgoD-like.
DR PANTHER; PTHR48080; PTHR48080; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR SFLD; SFLDF00005; glucarate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR TIGRFAMs; TIGR03247; glucar-dehydr; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Magnesium; Metal-binding;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9772162"
FT CHAIN 2..446
FT /note="Glucarate dehydratase"
FT /id="PRO_0000171264"
FT ACT_SITE 207
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:11513584"
FT ACT_SITE 339
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:11513584"
FT BINDING 32
FT /ligand="substrate"
FT BINDING 103
FT /ligand="substrate"
FT BINDING 150
FT /ligand="substrate"
FT BINDING 205
FT /ligand="substrate"
FT BINDING 235..237
FT /ligand="substrate"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11513584"
FT BINDING 266
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11513584"
FT BINDING 289
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11513584"
FT BINDING 289
FT /ligand="substrate"
FT BINDING 339..341
FT /ligand="substrate"
FT BINDING 368
FT /ligand="substrate"
FT BINDING 422
FT /ligand="substrate"
FT MUTAGEN 150
FT /note="Y->F: Reduces activity 100-fold."
FT /evidence="ECO:0000269|PubMed:10769114"
FT MUTAGEN 207
FT /note="K->Q: Reduces activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:10769114"
FT MUTAGEN 207
FT /note="K->R: Reduces activity 10000-fold."
FT /evidence="ECO:0000269|PubMed:10769114"
FT MUTAGEN 339
FT /note="H->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:10769114"
FT MUTAGEN 339
FT /note="H->N: Reduces activity 10000-fold."
FT /evidence="ECO:0000269|PubMed:10769114"
FT MUTAGEN 339
FT /note="H->Q: Reduces activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:10769114"
FT MUTAGEN 341
FT /note="N->D: Inactive in the dehydration reaction of D-
FT glucarate, L-idarate, and 4F-Gluc."
FT /evidence="ECO:0000269|PubMed:11513584"
FT MUTAGEN 341
FT /note="N->L: Almost no effect on the dehydration reaction
FT of D-glucarate, L-idarate, and 4F-Gluc."
FT /evidence="ECO:0000269|PubMed:11513584"
FT MUTAGEN 366
FT /note="D->A,N: Reduces activity over 100-fold."
FT /evidence="ECO:0000269|PubMed:10769114"
FT CONFLICT 310..313
FT /note="PLAD -> RWRI (in Ref. 1; AAB40437)"
FT /evidence="ECO:0000305"
FT STRAND 9..21
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 34..45
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 80..90
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:1EC8"
FT TURN 96..99
FT /evidence="ECO:0007829|PDB:1EC8"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 109..128
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:1ECQ"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 143..147
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 160..162
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 185..199
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 202..207
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 209..211
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 213..226
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 230..235
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 242..251
FT /evidence="ECO:0007829|PDB:1EC7"
FT TURN 252..255
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 256..261
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 271..282
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 286..291
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 295..304
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 308..311
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 314..317
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 319..331
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 345..356
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 369..372
FT /evidence="ECO:0007829|PDB:1EC7"
FT TURN 373..375
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 378..381
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 389..391
FT /evidence="ECO:0007829|PDB:1EC7"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 404..416
FT /evidence="ECO:0007829|PDB:1EC7"
FT HELIX 425..429
FT /evidence="ECO:0007829|PDB:1EC7"
SQ SEQUENCE 446 AA; 49141 MW; DFB07C9CA33F542C CRC64;
MSSQFTTPVV TEMQVIPVAG HDSMLMNLSG AHAPFFTRNI VIIKDNSGHT GVGEIPGGEK
IRKTLEDAIP LVVGKTLGEY KNVLTLVRNT FADRDAGGRG LQTFDLRTTI HVVTGIEAAM
LDLLGQHLGV NVASLLGDGQ QRSEVEMLGY LFFVGNRKAT PLPYQSQPDD SCDWYRLRHE
EAMTPDAVVR LAEAAYEKYG FNDFKLKGGV LAGEEEAESI VALAQRFPQA RITLDPNGAW
SLNEAIKIGK YLKGSLAYAE DPCGAEQGFS GREVMAEFRR ATGLPTATNM IATDWRQMGH
TLSLQSVDIP LADPHFWTMQ GSVRVAQMCH EFGLTWGSHS NNHFDISLAM FTHVAAAAPG
KITAIDTHWI WQEGNQRLTK EPFEIKGGLV QVPEKPGLGV EIDMDQVMKA HELYQKHGLG
ARDDAMGMQY LIPGWTFDNK RPCMVR
