EzCatDB: D00261

DB codeD00261
RLCP classification8.131.712490.370
5.14.3200000.372
8.113.901890.372
CATH domainDomain 13.30.390.10
Domain 23.20.20.120Catalytic domain
E.C.4.2.1.40
CSA1ec9

CATH domainRelated DB codes (homologues)
3.20.20.120D00273,D00282,D00283
3.30.390.10D00273,D00282,D00283

Enzyme Name
Swiss-protKEGG

P42206P0AES2
Protein nameGlucarate dehydrataseGlucarate dehydrataseglucarate dehydratase
D-glucarate dehydratase
D-glucarate hydro-lyase
SynonymsGDH
GlucD
EC 4.2.1.40
GDH
GlucD
EC 4.2.1.40

KEGG pathways
MAP codePathways
MAP00053Ascorbate and aldarate metabolism

Swiss-prot:Accession NumberP42206P0AES2
Entry nameGUDH_PSEPUGUDH_ECOLI
ActivityD-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.
SubunitHomotetramer.
Subcellular location

CofactorMagnesium (By similarity).Magnesium.


CofactorsSubstratesProductsintermediates
KEGG-idC00305C00818C00679C00001I00072I00073
CompoundMagnesiumD-Glucarate5-Dehydro-4-deoxy-D-glucarateH2O5,6-enediol-D-glucarate4,5-enol-4-deoxy-D-glucarate
Typedivalent metal (Ca2+, Mg2+)carbohydrate,carboxyl groupcarbohydrate,carboxyl groupH2O

1bqgA01UnboundUnboundUnbound
UnboundUnbound
1ec7A01UnboundUnboundUnbound
UnboundUnbound
1ec7B01UnboundUnboundUnbound
UnboundUnbound
1ec7C01UnboundUnboundUnbound
UnboundUnbound
1ec7D01UnboundUnboundUnbound
UnboundUnbound
1ec8A01UnboundUnboundUnbound
UnboundUnbound
1ec8B01UnboundUnboundUnbound
UnboundUnbound
1ec8C01UnboundUnboundUnbound
UnboundUnbound
1ec8D01UnboundUnboundUnbound
UnboundUnbound
1ec9A01UnboundUnboundUnbound
UnboundUnbound
1ec9B01UnboundUnboundUnbound
UnboundUnbound
1ec9C01UnboundUnboundUnbound
UnboundUnbound
1ec9D01UnboundUnboundUnbound
UnboundUnbound
1ecqA01UnboundUnboundUnbound
UnboundUnbound
1ecqB01UnboundUnboundUnbound
UnboundUnbound
1ecqC01UnboundUnboundUnbound
UnboundUnbound
1ecqD01UnboundUnboundUnbound
UnboundUnbound
1jctA01UnboundUnboundUnbound
UnboundUnbound
1jctB01UnboundUnboundUnbound
UnboundUnbound
1jdfA01UnboundUnboundUnbound
UnboundUnbound
1jdfB01UnboundUnboundUnbound
UnboundUnbound
1jdfC01UnboundUnboundUnbound
UnboundUnbound
1jdfD01UnboundUnboundUnbound
UnboundUnbound
1bqgA02UnboundUnboundUnbound
UnboundUnbound
1ec7A02Bound:_MGUnboundUnbound
UnboundUnbound
1ec7B02Bound:_MGUnboundUnbound
UnboundUnbound
1ec7C02Bound:_MGUnboundUnbound
UnboundUnbound
1ec7D02Bound:_MGUnboundUnbound
UnboundUnbound
1ec8A02Bound:_MGUnboundBound:GLR
UnboundUnbound
1ec8B02Bound:_MGUnboundBound:GLR
UnboundUnbound
1ec8C02Bound:_MGUnboundBound:GLR
UnboundUnbound
1ec8D02Bound:_MGUnboundBound:GLR
UnboundUnbound
1ec9A02Bound:_MGUnboundUnbound
Intermediate-analogue:XYHUnbound
1ec9B02Bound:_MGUnboundUnbound
Intermediate-analogue:XYHUnbound
1ec9C02Bound:_MGUnboundUnbound
Intermediate-analogue:XYHUnbound
1ec9D02Bound:_MGUnboundUnbound
Intermediate-analogue:XYHUnbound
1ecqA02Bound:_MGUnboundUnbound
UnboundIntermediate-bound:DXG
1ecqB02Bound:_MGUnboundUnbound
UnboundIntermediate-bound:DXG
1ecqC02Bound:_MGUnboundUnbound
UnboundIntermediate-bound:DXG
1ecqD02Bound:_MGUnboundUnbound
UnboundIntermediate-bound:DXG
1jctA02Bound:_MGBound:GKRUnbound
UnboundUnbound
1jctB02Bound:_MGBound:GKRUnbound
UnboundUnbound
1jdfA02Bound:_MGUnboundBound:GLR
UnboundUnbound
1jdfB02Bound:_MGUnboundBound:GLR
UnboundUnbound
1jdfC02Bound:_MGUnboundBound:GLR
UnboundUnbound
1jdfD02Bound:_MGUnboundBound:GLR
UnboundUnbound

Active-site residues
resource
literature [2], [4], [5]
pdbCatalytic residuesCofactor-binding residuescomment
1bqgA01


1ec7A01


1ec7B01


1ec7C01


1ec7D01


1ec8A01


1ec8B01


1ec8C01


1ec8D01


1ec9A01


1ec9B01


1ec9C01


1ec9D01


1ecqA01


1ecqB01


1ecqC01


1ecqD01


1jctA01


1jctB01


1jdfA01


1jdfB01


1jdfC01


1jdfD01


1bqgA02TYR 156;LYS 213;ASP 319;HIS 345
ASP 241;GLU 266;ASN 295(Magnesium binding)

1ec7A02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec7B02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec7C02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec7D02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8A02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8B02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8C02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec8D02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9A02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9B02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9C02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ec9D02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqA02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqB02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqC02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1ecqD02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)

1jctA02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)
mutant N341L
1jctB02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)
mutant N341L
1jdfA02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)
mutant N341D
1jdfB02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)
mutant N341D
1jdfC02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)
mutant N341D
1jdfD02TYR 150;LYS 207;ASP 313;HIS 339
ASP 235;GLU 260;ASN 289(Magnesium binding)
mutant N341D

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.16496
[2]Scheme 2, p.14365-143674
[4]Scheme 1, p.4596-46013
[5]Scheme 1, p.100583

references
[1]
PubMed ID8987982
JournalBiochemistry
Year1996
Volume35
Pages16489-501
AuthorsBabbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA
TitleThe enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
[2]
CommentsX-ray crystallography
PubMed ID9772161
JournalBiochemistry
Year1998
Volume37
Pages14358-68
AuthorsGulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I
TitleEvolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
Related PDB1bqg
[3]
PubMed ID9772160
JournalBiochemistry
Year1998
Volume37
Pages14350-7
AuthorsPalmer DR, Hubbard BK, Gerlt JA
TitleEvolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS)
Medline ID98447506
PubMed ID10769114
JournalBiochemistry
Year2000
Volume39
Pages4590-602
AuthorsGulick AM, Hubbard BK, Gerlt JA, Rayment I
TitleEvolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
Related PDB1ec7,1ec8,1ec9,1ecq
Related Swiss-protP42206
[5]
PubMed ID11513584
JournalBiochemistry
Year2001
Volume40
Pages10054-62
AuthorsGulick AM, Hubbard BK, Gerlt JA, Rayment I
TitleEvolution 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 PDB1jct,1jdf

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.

createdupdated
2004-07-012011-06-06
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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