DB code: D00261

RLCP classification 8.131.712490.370 : Isomerization
5.14.3200000.372 : Elimination
8.113.901890.372 : Isomerization
CATH domain 3.30.390.10 : Enolase-like; domain 1
3.20.20.120 : TIM Barrel Catalytic domain
E.C. 4.2.1.40
CSA 1ec9
M-CSA 1ec9
MACiE

CATH domain Related DB codes (homologues)
3.20.20.120 : TIM Barrel D00273 D00282 D00283
3.30.390.10 : Enolase-like; domain 1 D00273 D00282 D00283

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P42206 Glucarate dehydratase
GDH
GlucD
EC 4.2.1.40
PF01188 (MR_MLE)
PF02746 (MR_MLE_N)
[Graphical View]
P0AES2 Glucarate dehydratase
GDH
GlucD
EC 4.2.1.40
PF01188 (MR_MLE)
[Graphical View] 		NP_417267.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490995.1 (Protein)
NC_007779.1 (DNA/RNA sequence)

KEGG enzyme name
glucarate dehydratase
D-glucarate dehydratase
D-glucarate hydro-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P42206 GUDH_PSEPU D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O. Homotetramer. Magnesium (By similarity).
P0AES2 GUDH_ECOLI D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O. Magnesium.

KEGG Pathways
Map code Pathways E.C.
MAP00053 Ascorbate and aldarate metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00818 C00679 C00001 I00072 I00073
E.C.
Compound Magnesium D-Glucarate 5-Dehydro-4-deoxy-D-glucarate H2O 5,6-enediol-D-glucarate 4,5-enol-4-deoxy-D-glucarate
Type divalent metal (Ca2+, Mg2+) carbohydrate,carboxyl group carbohydrate,carboxyl group H2O
ChEBI 18420
 18420
 		16002
 16002
 		16369
 16369
 		15377
 15377
PubChem 888
 888
 		33037
 607
 33037
 607
 		439290
 439290
 		22247451
 962
 22247451
 962
1bqgA01 Unbound Unbound Unbound Unbound Unbound
1ec7A01 Unbound Unbound Unbound Unbound Unbound
1ec7B01 Unbound Unbound Unbound Unbound Unbound
1ec7C01 Unbound Unbound Unbound Unbound Unbound
1ec7D01 Unbound Unbound Unbound Unbound Unbound
1ec8A01 Unbound Unbound Unbound Unbound Unbound
1ec8B01 Unbound Unbound Unbound Unbound Unbound
1ec8C01 Unbound Unbound Unbound Unbound Unbound
1ec8D01 Unbound Unbound Unbound Unbound Unbound
1ec9A01 Unbound Unbound Unbound Unbound Unbound
1ec9B01 Unbound Unbound Unbound Unbound Unbound
1ec9C01 Unbound Unbound Unbound Unbound Unbound
1ec9D01 Unbound Unbound Unbound Unbound Unbound
1ecqA01 Unbound Unbound Unbound Unbound Unbound
1ecqB01 Unbound Unbound Unbound Unbound Unbound
1ecqC01 Unbound Unbound Unbound Unbound Unbound
1ecqD01 Unbound Unbound Unbound Unbound Unbound
1jctA01 Unbound Unbound Unbound Unbound Unbound
1jctB01 Unbound Unbound Unbound Unbound Unbound
1jdfA01 Unbound Unbound Unbound Unbound Unbound
1jdfB01 Unbound Unbound Unbound Unbound Unbound
1jdfC01 Unbound Unbound Unbound Unbound Unbound
1jdfD01 Unbound Unbound Unbound Unbound Unbound
1bqgA02 Unbound Unbound Unbound Unbound Unbound
1ec7A02 Bound:_MG Unbound Unbound Unbound Unbound
1ec7B02 Bound:_MG Unbound Unbound Unbound Unbound
1ec7C02 Bound:_MG Unbound Unbound Unbound Unbound
1ec7D02 Bound:_MG Unbound Unbound Unbound Unbound
1ec8A02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1ec8B02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1ec8C02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1ec8D02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1ec9A02 Bound:_MG Unbound Unbound Intermediate-analogue:XYH Unbound
1ec9B02 Bound:_MG Unbound Unbound Intermediate-analogue:XYH Unbound
1ec9C02 Bound:_MG Unbound Unbound Intermediate-analogue:XYH Unbound
1ec9D02 Bound:_MG Unbound Unbound Intermediate-analogue:XYH Unbound
1ecqA02 Bound:_MG Unbound Unbound Unbound Intermediate-bound:DXG
1ecqB02 Bound:_MG Unbound Unbound Unbound Intermediate-bound:DXG
1ecqC02 Bound:_MG Unbound Unbound Unbound Intermediate-bound:DXG
1ecqD02 Bound:_MG Unbound Unbound Unbound Intermediate-bound:DXG
1jctA02 Bound:_MG Bound:GKR Unbound Unbound Unbound
1jctB02 Bound:_MG Bound:GKR Unbound Unbound Unbound
1jdfA02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1jdfB02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1jdfC02 Bound:_MG Unbound Bound:GLR Unbound Unbound
1jdfD02 Bound:_MG Unbound Bound:GLR Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2], [4], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bqgA01
1ec7A01
1ec7B01
1ec7C01
1ec7D01
1ec8A01
1ec8B01
1ec8C01
1ec8D01
1ec9A01
1ec9B01
1ec9C01
1ec9D01
1ecqA01
1ecqB01
1ecqC01
1ecqD01
1jctA01
1jctB01
1jdfA01
1jdfB01
1jdfC01
1jdfD01
1bqgA02 TYR 156;LYS 213;ASP 319;HIS 345 ASP 241;GLU 266;ASN 295(Magnesium binding)
1ec7A02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec7B02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec7C02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec7D02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec8A02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec8B02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec8C02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec8D02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec9A02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec9B02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec9C02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ec9D02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ecqA02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ecqB02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ecqC02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1ecqD02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding)
1jctA02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding) mutant N341L
1jctB02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding) mutant N341L
1jdfA02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding) mutant N341D
1jdfB02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding) mutant N341D
1jdfC02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding) mutant N341D
1jdfD02 TYR 150;LYS 207;ASP 313;HIS 339 ASP 235;GLU 260;ASN 289(Magnesium binding) mutant N341D

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.16496
[2]
Scheme 2, p.14365-14367 4
[4]
Scheme 1, p.4596-4601 3
[5]
Scheme 1, p.10058 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 8987982
Journal Biochemistry
Year 1996
Volume 35
Pages 16489-501
Authors Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA
Title The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9772161
Journal Biochemistry
Year 1998
Volume 37
Pages 14358-68
Authors Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I
Title Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
Related PDB 1bqg
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9772160
Journal Biochemistry
Year 1998
Volume 37
Pages 14350-7
Authors Palmer DR, Hubbard BK, Gerlt JA
Title Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS)
Medline ID 98447506
PubMed ID 10769114
Journal Biochemistry
Year 2000
Volume 39
Pages 4590-602
Authors Gulick AM, Hubbard BK, Gerlt JA, Rayment I
Title Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
Related PDB 1ec7 1ec8 1ec9 1ecq
Related UniProtKB P42206
[5]
Resource
Comments
Medline ID
PubMed ID 11513584
Journal Biochemistry
Year 2001
Volume 40
Pages 10054-62
Authors Gulick AM, Hubbard BK, Gerlt JA, Rayment I
Title 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.
Related PDB 1jct 1jdf
Related UniProtKB

Comments
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.

Created Updated
2004-07-01 2011-06-06