D00261
type: Enzyme
rlcp: p370
rlcp: p372
cath: Enolase-like; domain 1
cath: TIM Barrel
ec: https://purl.uniprot.org/enzyme/4.2.1.40
csa: 1ec9
uniprot: P42206
uniprot: P0AES2
kegg enzyme: glucarate dehydratase
kegg enzyme: D-glucarate dehydratase
kegg enzyme: D-glucarate hydro-lyase
kegg pathway: Ascorbate and aldarate metabolism
kegg cofactor: Magnesium
kegg substrate: D-Glucarate
kegg product: 5-Dehydro-4-deoxy-D-glucarate
kegg product: H2O
kegg intermediate: 5,6-enediol-D-glucarate
kegg intermediate: 4,5-enol-4-deoxy-D-glucarate
pdb: 1bqgA01
pdb: 1ec7A01
pdb: 1ec7B01
pdb: 1ec7C01
pdb: 1ec7D01
pdb: 1ec8A01
pdb: 1ec8B01
pdb: 1ec8C01
pdb: 1ec8D01
pdb: 1ec9A01
pdb: 1ec9B01
pdb: 1ec9C01
pdb: 1ec9D01
pdb: 1ecqA01
pdb: 1ecqB01
pdb: 1ecqC01
pdb: 1ecqD01
pdb: 1jctA01
pdb: 1jctB01
pdb: 1jdfA01
pdb: 1jdfB01
pdb: 1jdfC01
pdb: 1jdfD01
pdb: 1bqgA02
pdb: 1ec7A02
pdb: 1ec7B02
pdb: 1ec7C02
pdb: 1ec7D02
pdb: 1ec8A02
pdb: 1ec8B02
pdb: 1ec8C02
pdb: 1ec8D02
pdb: 1ec9A02
pdb: 1ec9B02
pdb: 1ec9C02
pdb: 1ec9D02
pdb: 1ecqA02
pdb: 1ecqB02
pdb: 1ecqC02
pdb: 1ecqD02
pdb: 1jctA02
pdb: 1jctB02
pdb: 1jdfA02
pdb: 1jdfB02
pdb: 1jdfC02
pdb: 1jdfD02
pdb bound state: Unbound
  compound: D-Glucarate
  pdb: 1bqgA01
pdb bound state: Unbound
  compound: D-Glucarate
  pdb: 1ec7A01
pdb bound state: Unbound
  compound: D-Glucarate
  pdb: 1ec7B01
pdb bound state: Unbound
  compound: D-Glucarate
  pdb: 1ec7C01
pdb bound state: Unbound
  compound: D-Glucarate
  pdb: 1ec7D01
pdb bound state: Unbound
  compound: D-Glucarate
  pdb: 1ec8A01
active site residues resources: Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
active site residues resources: Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli.
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/D00261#6
references: The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
references: Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
references: Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
references: Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
references: Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli.
comment: This enzyme belongs to the enolase superfamily. This enzyme catalyzes dehydration of either D-glucarate or L-idarate to form 5-Dehydro-4-deoxy-D-glucarate (KDG). According to the literature [2], [4] & [5], the catalytic reaction proceeds as follows: (A) Isomerization (change in the position of double-bond): (A1) A general base abstracts the alpha-proton from the C5 carbon, resulting in the formation of the enediolate anion intermediate. Here, His339 (of 1ec7) acts as the R-specific base for the D-glucarate substrate, whilst Lys207 acts as the S-specific base for the L-idarate (see [4] & [5]). (A2) The enediolate anion is stabilized by the manesium ion, which is coordinated by Asp235, Glu266 and Asn289. (B) Elimination of hydroxyl group from the substrate: (B1) A general acid eliminates the 4-OH group from the enediolate anion intermediate, by donating a proton to the group, resulting in the formation of an enol intermediate, in which a double bond is formed between the C4 and the C5 carbon atoms. Although the earlier paper [3] mentioned that Tyr150 may act as the general acid, more recent papers [4] & [5] proposed that His339 would act as the general acid. (B2) The enol intermediate might be stabilized by Tyr150, Lys205 and Asn237, as well as the magnesium ion (see [4]). The enol oxygen is stabilized by Tyr150, whereas the carboxylate is stabilized by Lys205, Asn237 and the magnesium ion. (C) Isomerization (change in the position of double-bond): (C0) The enol oxygen is stabilized by Tyr150, whereas the carboxylate is stabilized by Lys205, Asn237 and the magnesium ion. (C1) Another general acid donates a proton to the C4 carbon of the enol intermediate, leading to its tautomerization and to the final product, KDG. According to the paper [5], His339 acts as the second acid, as well.

Enolase-like; domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.30.390.10

TIM Barrel
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.20.20.120
catalytic domain: index.html

Ascorbate and aldarate metabolism
type: KeggPathway
references: KEGG:MAP00053

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

D-Glucarate
type: KeggSubstrate
references: KEGG:C00818
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:16002
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

5-Dehydro-4-deoxy-D-glucarate
type: KeggProduct
references: KEGG:C00679
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:16369
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H2O
type: KeggProduct
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

5,6-enediol-D-glucarate
type: KeggIntermediate
references: KEGG:I00072

4,5-enol-4-deoxy-D-glucarate
type: KeggIntermediate
references: KEGG:I00073

1bqgA02
type: Pdb
references: 1bqg
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bqg
catalytic residue: TYR 156;LYS 213;ASP 319;HIS 345
cofactor binding residue: ASP 241;GLU 266;ASN 295(Magnesium binding)

1ec7A02
type: Pdb
references: 1ec7
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec7
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec7B02
type: Pdb
references: 1ec7
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec7
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec7C02
type: Pdb
references: 1ec7
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec7
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec7D02
type: Pdb
references: 1ec7
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec7
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8A02
type: Pdb
references: 1ec8
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec8
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8B02
type: Pdb
references: 1ec8
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec8
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8C02
type: Pdb
references: 1ec8
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec8
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8D02
type: Pdb
references: 1ec8
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec8
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9A02
type: Pdb
references: 1ec9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec9
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9B02
type: Pdb
references: 1ec9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec9
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9C02
type: Pdb
references: 1ec9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec9
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9D02
type: Pdb
references: 1ec9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ec9
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqA02
type: Pdb
references: 1ecq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ecq
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqB02
type: Pdb
references: 1ecq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ecq
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqC02
type: Pdb
references: 1ecq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ecq
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqD02
type: Pdb
references: 1ecq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ecq
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)

1jctA02
type: Pdb
references: 1jct
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jct
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)
comment: mutant N341L

1jctB02
type: Pdb
references: 1jct
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jct
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)
comment: mutant N341L

1jdfA02
type: Pdb
references: 1jdf
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jdf
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)
comment: mutant N341D

1jdfB02
type: Pdb
references: 1jdf
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jdf
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)
comment: mutant N341D

1jdfC02
type: Pdb
references: 1jdf
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jdf
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)
comment: mutant N341D

1jdfD02
type: Pdb
references: 1jdf
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jdf
catalytic residue: TYR 150;LYS 207;ASP 313;HIS 339
cofactor binding residue: ASP 235;GLU 260;ASN 289(Magnesium binding)
comment: mutant N341D

The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8987982
journal: Biochemistry
volume: 35
pages: 16489-501
published year: 1996
authors:
  item: Babbitt PC
  item: Hasson MS
  item: Wedekind JE
  item: Palmer DR
  item: Barrett WC
  item: Reed GH
  item: Rayment I
  item: Ringe D
  item: Kenyon GL
  item: Gerlt JA

Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/9772161
journal: Biochemistry
volume: 37
pages: 14358-68
published year: 1998
authors:
  item: Gulick AM
  item: Palmer DR
  item: Babbitt PC
  item: Gerlt JA
  item: Rayment I
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9772160
journal: Biochemistry
volume: 37
pages: 14350-7
published year: 1998
authors:
  item: Palmer DR
  item: Hubbard BK
  item: Gerlt JA

Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS)
medline id: 98447506
references: http://www.ncbi.nlm.nih.gov/pubmed/10769114
journal: Biochemistry
volume: 39
pages: 4590-602
published year: 2000
authors:
  item: Gulick AM
  item: Hubbard BK
  item: Gerlt JA
  item: Rayment I
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P42206

Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11513584
journal: Biochemistry
volume: 40
pages: 10054-62
published year: 2001
authors:
  item: Gulick AM
  item: Hubbard BK
  item: Gerlt JA
  item: Rayment I
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

IntermediateAnalogue
compound: 5,6-enediol-D-glucarate
pdb: 1ec9A02
ligand het code: XYH

IntermediateAnalogue
compound: 5,6-enediol-D-glucarate
pdb: 1ec9B02
ligand het code: XYH

IntermediateAnalogue
compound: 5,6-enediol-D-glucarate
pdb: 1ec9C02
ligand het code: XYH

IntermediateAnalogue
compound: 5,6-enediol-D-glucarate
pdb: 1ec9D02
ligand het code: XYH

IntermediateBound
compound: 4,5-enol-4-deoxy-D-glucarate
pdb: 1ecqA02
ligand het code: DXG

IntermediateBound
compound: 4,5-enol-4-deoxy-D-glucarate
pdb: 1ecqB02
ligand het code: DXG

IntermediateBound
compound: 4,5-enol-4-deoxy-D-glucarate
pdb: 1ecqC02
ligand het code: DXG

IntermediateBound
compound: 4,5-enol-4-deoxy-D-glucarate
pdb: 1ecqD02
ligand het code: DXG

ReferenceForCatalyticMechanism
reference index: 1
reference section: p.16496

ReferenceForCatalyticMechanism
reference index: 2
reference section: Scheme 2, p.14365-14367
reference step: 4

ReferenceForCatalyticMechanism
reference index: 4
reference section: Scheme 1, p.4596-4601
reference step: 3

ReferenceForCatalyticMechanism
reference index: 5
reference section: Scheme 1, p.10058
reference step: 3