PDBsum entry 2dw6

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Jmol PyMol
Protein chains
388 a.a. *
TAR ×3
_MG ×4
Waters ×466
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the mutant k184a of d-tartrate dehydratase from bradyrhizobium japonicum complexed with mg++ and d-tartrate
Structure: Bll6730 protein. Chain: a, b, c, d. Synonym: d-tartrate dehydratase. Engineered: yes. Mutation: yes
Source: Bradyrhizobium japonicum. Organism_taxid: 375. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.30Å     R-factor:   0.209     R-free:   0.232
Authors: A.A.Fedorov,E.V.Fedorov,W.S.Yew,B.M.Wood,J.A.Gerlt,S.C.Almo
Key ref:
W.S.Yew et al. (2006). Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum. Biochemistry, 45, 14598-14608. PubMed id: 17144653 DOI: 10.1021/bi061688g
07-Aug-06     Release date:   19-Dec-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q89FH0  (Q89FH0_BRAJA) -  D(-)-tartrate dehydratase
389 a.a.
388 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - D(-)-tartrate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S,S)-tartrate = oxaloacetate + H2O
Bound ligand (Het Group name = TAR)
corresponds exactly
= oxaloacetate
+ H(2)O
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein homooligomerization   1 term 
  Biochemical function     lyase activity     4 terms  


    Added reference    
DOI no: 10.1021/bi061688g Biochemistry 45:14598-14608 (2006)
PubMed id: 17144653  
Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.
W.S.Yew, A.A.Fedorov, E.V.Fedorov, B.M.Wood, S.C.Almo, J.A.Gerlt.
We focus on the assignment of function to and elucidation of structure-function relationships for a member of the mechanistically diverse enolase superfamily encoded by the Bradyrhizobium japonicum genome (bll6730; GI:27381841). As suggested by sequence alignments, the active site contains the same functional groups found in the active site of mandelate racemase (MR) that catalyzes a 1,1-proton transfer reaction: two acid/base catalysts, Lys 184 at the end of the second beta-strand, and a His 322-Asp 292 dyad at the ends of the seventh and sixth beta-strands, respectively, as well as ligands for an essential Mg2+, Asp 213, Glu 239, and Glu 265 at the ends of the third, fourth, and fifth beta-strands, respectively. We screened a library of 46 acid sugars and discovered that only d-tartrate is dehydrated, yielding oxaloacetate as product. The kinetic constants (kcat = 7.3 s(-1); kcat/KM = 8.5 x 10(4) M(-1) s(-1)) are consistent with assignment of the d-tartrate dehydratase (TarD) function. The kinetic phenotypes of mutants as well as the structures of liganded complexes are consistent with a mechanism in which Lys 184 initiates the reaction by abstraction of the alpha-proton to generate a Mg2+-stabilized enediolate intermediate, and the vinylogous beta-elimination of the 3-OH group is general acid-catalyzed by the His 322, accomplishing the anti-elimination of water. The replacement of the leaving group by solvent-derived hydrogen is stereorandom, suggesting that the enol tautomer of oxaloacetate is the product; this expectation was confirmed by its observation by 1H NMR spectroscopy. Thus, the TarD-catalyzed reaction is a "simple" extension of the two-step reaction catalyzed by MR: base-catalyzed proton abstraction to generate a Mg2+-stabilized enediolate intermediate followed by acid-catalyzed decomposition of that intermediate to yield the product.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19883118 J.F.Rakus, C.Kalyanaraman, A.A.Fedorov, E.V.Fedorov, F.P.Mills-Groninger, R.Toro, J.Bonanno, K.Bain, J.M.Sauder, S.K.Burley, S.C.Almo, M.P.Jacobson, and J.A.Gerlt (2009).
Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .
  Biochemistry, 48, 11546-11558.
PDB codes: 2oqy 3es7 3es8 3fyy 3hpf
  20948600 S.D.Copley (2009).
Prediction of function in protein superfamilies.
  F1000 Biol Rep, 1, 0.  
19219566 U.Pieper, R.Chiang, J.J.Seffernick, S.D.Brown, M.E.Glasner, L.Kelly, N.Eswar, J.M.Sauder, J.B.Bonanno, S.Swaminathan, S.K.Burley, X.Zheng, M.R.Chance, S.C.Almo, J.A.Gerlt, F.M.Raushel, M.P.Jacobson, P.C.Babbitt, and A.Sali (2009).
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
  J Struct Funct Genomics, 10, 107-125.  
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