Publications

• Crystallization of diaminopimelate decarboxylase from Escherichia coli, a stereospecific D-amino-acid decarboxylase.

  Momany C., Levdikov V., Blagova L., Crews K.

  The final step in lysine biosynthesis in bacteria, the conversion of meso-diaminopimelate to L-lysine, is catalyzed by the only known D-amino-acid decarboxylase, diaminopimelate decarboxylase (DDC). The Escherichia coli DDC has been cloned, overexpressed in E. coli with a carboxy-terminal polyhist ... >> More

  The final step in lysine biosynthesis in bacteria, the conversion of meso-diaminopimelate to L-lysine, is catalyzed by the only known D-amino-acid decarboxylase, diaminopimelate decarboxylase (DDC). The Escherichia coli DDC has been cloned, overexpressed in E. coli with a carboxy-terminal polyhistidine purification tag and crystallized from lithium sulfate. The protein is intensely yellow, owing to the pyridoxal-5'-phosphate cofactor, and is enzymatically active. Large well ordered crystals, belonging to space group P6(1)22 with unit-cell parameters a = b = 98.6, c = 177 A, make high-resolution X-ray diffraction studies possible to characterize the residues important in stereospecific decarboxylation and reprotonation during catalytic turnover. << Less

  Acta Crystallogr. D 58:549-552(2002) [PubMed] [EuropePMC]

• Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.

  Ray S.S., Bonanno J.B., Rajashankar K.R., Pinho M.G., He G., De Lencastre H., Tomasz A., Burley S.K.

  Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in ... >> More

  Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed. << Less

  Structure 10:1499-1508(2002) [PubMed] [EuropePMC]

• The catalytic intermediate stabilized by a 'down' active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis.

  Hu T., Wu D., Chen J., Ding J., Jiang H., Shen X.

  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 ... >> More

  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. << Less

  J. Biol. Chem. 283:21284-21293(2008) [PubMed] [EuropePMC]

• Purification and properties of diaminopimelate decarboxylase from Escherichia coli.

  White P.J., Kelly B.

  1. Diaminopimelate decarboxylase from a soluble extract of Escherichia coli A.T.C.C. 9637 was purified 200-fold by precipitation of nucleic acids, fractionation with acetone and then with ammonium sulphate, adsorption on calcium phosphate gel and chromatography on DEAE-cellulose or DEAE-Sephadex. ... >> More

  1. Diaminopimelate decarboxylase from a soluble extract of Escherichia coli A.T.C.C. 9637 was purified 200-fold by precipitation of nucleic acids, fractionation with acetone and then with ammonium sulphate, adsorption on calcium phosphate gel and chromatography on DEAE-cellulose or DEAE-Sephadex. 2. The purified enzyme showed only one component in the ultracentrifuge, with a sedimentation coefficient of 5.4s. One major peak and three much smaller peaks were observed on electrophoresis of the enzyme at pH8.9. 3. The mol.wt. of the enzyme was approx. 200000. The catalytic constant was 2000mol. of meso-diaminopimelic acid decomposed/min./mol. of enzyme, at 37 degrees . The relative rates of decarboxylation at 25 degrees , 37 degrees and 45 degrees were 0.17:1.0:1.6. At 37 degrees the Michaelis constant was 1.7mm and the optimum pH was 6.7-6.8. 4. There was an excess of acidic amino acids over basic amino acids in the enzyme, which was bound only on basic cellulose derivatives at pH6.8. 5. The enzyme had an absolute requirement for pyridoxal phosphate as a cofactor; no other derivative of pyridoxine had activity. A thiol compound (of which 2,3-dimercaptopropan-1-ol was the most effective) was also needed as an activator. 6. In the presence of 2,3-dimercaptopropan-1-ol (1mm), heavy-metal ions (Cu(2+), Hg(2+)) did not inhibit the enzyme, but there was inhibition by several amino acids with analogous structures to diaminopimelate, generally at high concentrations relative to the substrate. Penicillamine was inhibitory at relatively low concentrations; its action was prevented by pyridoxal phosphate. << Less

  Biochem. J. 96:75-84(1965) [PubMed] [EuropePMC]

• Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine.

  Deng X., Lee J., Michael A.J., Tomchick D.R., Goldsmith E.J., Phillips M.A.

  Pyridoxal 5'-phosphate (PLP)-dependent basic amino acid decarboxylases from the beta/alpha-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure dete ... >> More

  Pyridoxal 5'-phosphate (PLP)-dependent basic amino acid decarboxylases from the beta/alpha-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure determination of bacterial biosynthetic arginine decarboxylase (ADC) and carboxynorspermidine decarboxylase (CANSDC) to 2.3- and 2.0-A resolution, solved as product complexes with agmatine and norspermidine. Despite low overall sequence identity, the monomeric and dimeric structures are similar to other enzymes in the family, with the active sites formed between the beta/alpha-barrel domain of one subunit and the beta-barrel of the other. ADC contains both a unique interdomain insertion (4-helical bundle) and a C-terminal extension (3-helical bundle) and it packs as a tetramer in the asymmetric unit with the insertions forming part of the dimer and tetramer interfaces. Analytical ultracentrifugation studies confirmed that the ADC solution structure is a tetramer. Specificity for different basic amino acids appears to arise primarily from changes in the position of, and amino acid replacements in, a helix in the beta-barrel domain we refer to as the "specificity helix." Additionally, in CANSDC a key acidic residue that interacts with the distal amino group of other substrates is replaced by Leu(314), which interacts with the aliphatic portion of norspermidine. Neither product, agmatine in ADC nor norspermidine in CANSDC, form a Schiff base to pyridoxal 5'-phosphate, suggesting that the product complexes may promote product release by slowing the back reaction. These studies provide insight into the structural basis for the evolution of novel function within a common structural-fold. << Less

  J. Biol. Chem. 285:25708-25719(2010) [PubMed] [EuropePMC]

  This publication is cited by 2 other entries.

• Diaminopimelic acid decarboxylase in pyridoxin-deficient Escherichia coli.

  DENMAN R.F., HOARE D.S., WORK E.

  Biochim Biophys Acta 16:442-443(1955) [PubMed] [EuropePMC]