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PDBsum entry 1ecq

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1ecq
Jmol
Contents
Protein chains
444 a.a. *
Ligands
DXG ×4
IPA ×4
Metals
_MG ×4
Waters ×901
* Residue conservation analysis
PDB id:
1ecq
Name: Lyase
Title: E. Coli glucarate dehydratase bound to 4-deoxyglucarate
Structure: Glucarate dehydratase. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.209     R-free:   0.305
Authors: A.M.Gulick,B.K.Hubbard,J.A.Gerlt,I.Rayment
Key ref:
A.M.Gulick et al. (2000). Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli. Biochemistry, 39, 4590-4602. PubMed id: 10769114 DOI: 10.1021/bi992782i
Date:
25-Jan-00     Release date:   23-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AES2  (GUDD_ECOLI) -  Glucarate dehydratase
Seq:
Struc:
446 a.a.
444 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.40  - Glucarate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O
D-glucarate
=
5-dehydro-4-deoxy-D-glucarate
Bound ligand (Het Group name = DXG)
corresponds exactly
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi992782i Biochemistry 39:4590-4602 (2000)
PubMed id: 10769114  
 
 
Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
A.M.Gulick, B.K.Hubbard, J.A.Gerlt, I.Rayment.
 
  ABSTRACT  
 
D-Glucarate dehydratase (GlucD) from Escherichia coli catalyzes the dehydration of both D-glucarate and L-idarate as well as their interconversion via epimerization. GlucD is a member of the mandelate racemase (MR) subgroup of the enolase superfamily, the members of which catalyze reactions that are initiated by abstraction of the alpha-proton of a carboxylate anion substrate. Alignment of the sequence of GlucD with that of MR reveals a conserved Lys-X-Lys motif and a His-Asp dyad homologous to the S- and R-specific bases in the active site of MR. Crystals of GlucD have been obtained into which the substrate D-glucarate and two competitive inhibitors, 4-deoxy-D-glucarate and xylarohydroxamate, could be diffused; D-glucarate is converted to the dehydration product, 5-keto-4-deoxy-D-glucarate (KDG). The structures of these complexes have been determined and reveal the identities of the ligands for the required Mg(2+) (Asp(235), Glu(266), and Asn(289)) as well as confirm the expected presence of Lys(207) and His(339), the catalytic bases that are properly positioned to abstract the proton from C5 of L-idarate and D-glucarate, respectively. Surprisingly, the C6 carboxylate group of KDG is a bidentate ligand to the Mg(2+), with the resulting geometry of the bound KDG suggesting that stereochemical roles of Lys(207) and His(339) are reversed from the predictions made on the basis of the established structure-function relationships for the MR-catalyzed reaction. The catalytic roles of these residues have been examined by characterization of mutant enzymes, although we were unable to use these to demonstrate the catalytic independence of Lys(207) and His(339) as was possible for the homologous Lys(166) and His(297) in the MR-catalyzed reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18364348 A.Aghaie, C.Lechaplais, P.Sirven, S.Tricot, M.Besnard-Gonnet, D.Muselet, V.de Berardinis, A.Kreimeyer, G.Gyapay, M.Salanoubat, and A.Perret (2008).
New insights into the alternative D-glucarate degradation pathway.
  J Biol Chem, 283, 15638-15646.  
18754693 J.F.Rakus, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, B.K.Hubbard, J.D.Delli, P.C.Babbitt, S.C.Almo, and J.A.Gerlt (2008).
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
  Biochemistry, 47, 9944-9954.
PDB codes: 2i5q 3box 3cxo
18214979 M.Hayashida, S.H.Kim, K.Takeda, T.Hisano, and K.Miki (2008).
Crystal structure of N-acylamino acid racemase from Thermus thermophilus HB8.
  Proteins, 71, 519-523.
PDB code: 2zc8
16790929 J.A.Sundlov, J.A.Garringer, J.M.Carney, A.S.Reger, E.J.Drake, W.L.Duax, and A.M.Gulick (2006).
Determination of the crystal structure of EntA, a 2,3-dihydro-2,3-dihydroxybenzoic acid dehydrogenase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 62, 734-740.
PDB code: 2fwm
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11063568 M.St Maurice, and S.L.Bearne (2000).
Reaction intermediate analogues for mandelate racemase: interaction between Asn 197 and the alpha-hydroxyl of the substrate promotes catalysis.
  Biochemistry, 39, 13324-13335.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.