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Structural basis of substrate specificity in thiamin diphosphate dependent decarboxylases
Author(s) -
Yep Alejandra,
Kneen Malea M,
Kenyon George L,
McLeish Michael J
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.4.a471-b
Subject(s) - cofactor , substrate (aquarium) , pseudomonas putida , chemistry , biochemistry , decarboxylation , stereochemistry , pyruvate decarboxylase , enzyme , active site , biology , ecology , alcohol dehydrogenase , catalysis
Pyruvate decarboxylase (PDC) from Zymomonas mobilis and Saccharomyces cerevisiae , benzoylformate decarboxylase (BFD) from Pseudomonas putida and indolepyruvate decarboxylase (IPDC) from Enterobacter cloacae are all thiamin diphosphate (ThDP)‐dependent enzymes that decarboxylate 2‐keto carboxylic acids. Although they display a relatively low sequence similarity and broadly different substrate spectra, the structures of these enzymes show a common homotetrameric structure. Recently we have expressed, purified and partially characterized two other ThDP‐dependent decarboxylases, the branched chain 2‐keto acid decarboxylase (KdcA) from Lactococcus lactis and the phenylpyruvate decarboxylase (PPDC) from Saccharomyces cerevisiae . In order to understand the structural basis for their substrate recognition we modeled the substrate‐bound structures of KdcA and PPDC. The comparison of the crystal structures of BFD, PDC and IPDC with the models of KdcA and PPDC highlighted the similarities in the cofactor binding region in ThDP‐dependent decarboxylases. On the other hand, it also revealed important differences among them regarding the nature of the substrate binding residues. We identified a set of residues that shape the substrate binding pocket and that vary in each of the five enzymes analyzed. There is a correlation between the increasing bulkiness of the lateral chain of this array of amino acids and the decreasing size of the preferred substrate. This work was supported by NSF EF‐0425719.