ORENZA : a database of ORphan ENZyme Activities

ORphan ENZyme ActivitiesSorted by :
   EC number
   classes of activity
   KEGG metabolism pathway
   year of creation
EC used by the NC-IUBMBSorted by :
   EC number
   classes of activity
   KEGG metabolism pathway
   year of creation

Search by   NC-IUBMB EC number
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EC is Orphan !
Common name :D(-)-tartrate dehydratase

Systematic name :(S,S)-tartrate hydro-lyase (oxaloacetate-forming)

Other names :D-tartrate dehydratase
(S,S)-tartrate hydro-lyase
Cofactors : Iron.

Comments :Requires Fe(2+) or Mn(2+). cf. EC L(+)-tartrate dehydratase.

Created :EC created 1986

BRENDA organisms :Bradyrhizobium japonicum
Pseudomonas sp.
Rhodobacter sphaeroides

Swiss-ProtNo protein sequences are associated with EC in Swiss-Prot

TrEMBLNo protein sequences are associated with EC in TrEMBL

Users Comments# 1 - Date : 2007-07-22
Author : John Gerlt
Comment and/or Sequence evidence : We have associated the D-tartrate dehydratase function with a family of proteins in the enolase superfamily. I have copied the abstract from PubMed. John Gerlt Biochemistry. 2006 Dec 12;45(49):14598-608.Click here to read Links Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum. Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA. Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA. 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.

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