Abstract
The meso-diaminopimelate decarboxylase (DAPDC, EC 4.1.1.20) catalyzes the final step of L-lysine biosynthesis in bacteria and is regarded as a target for the discovery of antibiotics. Here we report the 2.3A crystal structure of DAPDC from Helicobacter pylori (HpDAPDC). The structure, in which the product L-lysine forms a Schiff base with the cofactor pyridoxal 5'-phosphate, provides structural insight into the substrate specificity and catalytic mechanism of the enzyme, and implies that the carboxyl to be cleaved locates at the si face of the cofactor. To our knowledge, this might be the first reported external aldimine of DAPDC. Moreover, the active site loop of HpDAPDC is in a "down" conformation and shields the ligand from solvent. Mutations of Ile(148) from the loop greatly impaired the catalytic efficiency. Combining the structural analysis of the I148L mutant, we hypothesize that HpDAPDC adopts an induced-fit catalytic mechanism in which this loop cycles through "down" and "up" conformations to stabilize intermediates and release product, respectively. Our work is expected to provide clues for designing specific inhibitors of DAPDC.
Highlights
The meso-diaminopimelate decarboxylase (DAPDC, EC 4.1.1.20) catalyzes the final step of L-lysine biosynthesis in bacteria and is regarded as a target for the discovery of antibiotics
Combining the crystal structure of the I148L mutant and the results from previous studies, we propose that HpDAPDC adopts an induced-fit mechanism for catalysis in which the active site loop cycles through down and “up” conformations to stabilize intermediates and release product, respectively
10 mg/ml HpDAPDC solution was incubated with 5 mM L-lysine on ice overnight, and 1 l of the complex was mixed with 1 l of JULY 25, 2008
Summary
The structure, in which the product L-lysine forms a Schiff base with the cofactor pyridoxal 5-phosphate, provides structural insight into the substrate specificity and catalytic mechanism of the enzyme, and implies that the carboxyl to be cleaved locates at the si face of the cofactor. To our knowledge, this might be the first reported external aldimine of DAPDC. Combining the crystal structure of the I148L mutant and the results from previous studies, we propose that HpDAPDC adopts an induced-fit mechanism for catalysis in which the active site loop cycles through down and “up” conformations to stabilize intermediates and release product, respectively. Our work is expected to gain insight into the essential catalytic mechanism of HpDAPDC and provide clues for designing specific inhibitors
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