Crystallization of diaminopimelate decarboxylase from<i>Escherichia coli</i>, a stereospecific<scp>D</scp>-amino-acid decarboxylase

Momany, Cory; Levdikov, V.M.; Blagova, L.; Crews, Kristine R.

doi:10.1107/s0907444902000148

Cited by 12 publications

(9 citation statements)

References 23 publications

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“…DapDC is structurally very similar to eukaryotic ODCs [164,165,169] and, with the exception of a rotation of the C-terminal domain, to Bacillus stearothermophilus alanine racemase [13]. The structure of DapDC has been solved from various sources, such as Escherichia coli, Mycobacterium tuberculosis and Methanococcus jannaschii, both in its ligand-free form [209,210], and complexed with the product lysine [209][210][211] or with the substrate analog azalaic acid [211].…”

Section: Diaminopimelate Decarboxylase Alanine Racemasementioning

confidence: 99%

“…1D7K, 2.10 [165] 1F3T, 2.00 (putrescine) [170] 2TOD, 2.00 (eflornithine) [29] 1ORD, 3.00 [163] 1NJJ, 2.45 (G418) [180] 1QU4, 2.90 [29] 7ODC, 1.60 [164] Diaminopimelate decarboxylase (III) 1KNW, 2.10 [209] 1KO0, 2.20 (L-lysine) [209] 1TUF, 2.40 (azalaic acid) [211] 1HKW, 2.80 [210] 1HKV, 2.60 (L-lysine) [210] 1TWI, 2.00 (L-lysine) [211] Alanine racemase (III) 1SFT, 1.90 [13] 1BD0, 1.60 (alanine phosphonate) [222] 1XFC, 1.90 [217] 1EPV, 2.20 (D-cycloserine adduct) [221] 1RCQ, 1.45 [218] 1NIU, 2.20 (L-cycloserine adduct) [221] 1VFH, 2.00 [233] 1VFS, 1.90 (D-cycloserine) [233] 1VFT, 2.30 (L-cycloserine) [233] 2SFP, 1.90 (propionate) [223] Serine hydroxymethyltransferase (I) 1BJ4, 2.65 [250] 1DFO, 2.40 (L-glycine and 5-formyl tetrahydrofolate) [247] 1CJ0, 2.80 [248] 1KKP, 1.93 (L-serine) [249] 1EJI, 2.90 [246] 1KL1, 1.93 (L-glycine) [249] 1KKJ, 1.93 [249] Cystathionine γ-synthase (I) 1CS1, 1.50 [277] 1I41, 3.20 (APPA) [286] 1QGN, 2.90 [278] 1I43, 3.10 (PPCA) [286] 1I48, 3.25 (CTCPO) [286] Cystathionine β-lyase (I) 1CL1, 1.83 [294] 1CL2, 2.20 (L-aminoethoxyvinyl glicine) [284] ( 1IBJ, 2.30 [295] Cystathionine γ-lyase (I) 1N8P, 2.60 [276] Methionine γ-lyase (I) 1GC0, 1.70 …”

Section: Introductionmentioning

confidence: 99%

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Pyridoxal 5-Phosphate Enzymes as Targets for Therapeutic Agents

Amadasi¹,

Bertoldi²,

Contestabile³

et al. 2007

CMC

177

157

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The vitamin B(6)-derived pyridoxal 5'-phosphate (PLP) is the cofactor of enzymes catalyzing a large variety of chemical reactions mainly involved in amino acid metabolism. These enzymes have been divided in five families and fold types on the basis of evolutionary relationships and protein structural organization. Almost 1.5% of all genes in prokaryotes code for PLP-dependent enzymes, whereas the percentage is substantially lower in eukaryotes. Although about 4% of enzyme-catalyzed reactions catalogued by the Enzyme Commission are PLP-dependent, only a few enzymes are targets of approved drugs and about twenty are recognised as potential targets for drugs or herbicides. PLP-dependent enzymes for which there are already commercially available drugs are DOPA decarboxylase (involved in the Parkinson disease), GABA aminotransferase (epilepsy), serine hydroxymethyltransferase (tumors and malaria), ornithine decarboxylase (African sleeping sickness and, potentially, tumors), alanine racemase (antibacterial agents), and human cytosolic branched-chain aminotransferase (pathological states associated to the GABA/glutamate equilibrium concentrations). Within each family or metabolic pathway, the enzymes for which drugs have been already approved for clinical use are discussed first, reporting the enzyme structure, the catalytic mechanism, the mechanism of enzyme inactivation or modulation by substrate-like or transition state-like drugs, and on-going research for increasing specificity and decreasing side-effects. Then, PLP-dependent enzymes that have been recently characterized and proposed as drug targets are reported. Finally, the relevance of recent genomic analysis of PLP-dependent enzymes for the selection of drug targets is discussed.

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Section: Diaminopimelate Decarboxylase Alanine Racemasementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pyridoxal 5-Phosphate Enzymes as Targets for Therapeutic Agents

Amadasi¹,

Bertoldi²,

Contestabile³

et al. 2007

CMC

177

157

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“…For example, the asymmetric unit of DAPDC from Escherichia coli (PDB codes 1KNW and 1KO0) (Fig. 1A) (11), Thermotoga maritima (PDB code 2YXX), and Helicobacter pylori (PDB code 2QGH) (8) is a monomer; whereas DAPDC from Vibrio cholerae (PDB code 3N2B) adopts a tetramer (Fig. 1B).…”

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confidence: 99%

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

Peverelli

Costa

Kirby

et al. 2016

Journal of Biological Chemistry

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Diaminopimelate decarboxylase (DAPDC) catalyzes the final step in the diaminopimelate biosynthesis pathway of bacteria. The product of the reaction is the essential amino acid L-lysine, which is an important precursor for the synthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria. Accordingly, the enzyme is a promising antibacterial target. Previous structural studies demonstrate that DAPDC exists as monomers, dimers, and tetramers in the crystal state. However, the active oligomeric form has not yet been determined. We show using analytical ultracentrifugation, small angle x-ray scattering, and enzyme kinetic analyses in solution that the active form of DAPDC from Bacillus anthracis, Escherichia coli, Mycobacterium tuberculosis, and Vibrio cholerae is a dimer. The importance of dimerization was probed further by generating dimerization interface mutants (N381A and R385A) of V. cholerae DAPDC. Our studies indicate that N381A and R385A are significantly attenuated in catalytic activity, thus confirming that dimerization of DAPDC is essential for function. These findings provide scope for the development of new antibacterial agents that prevent DAPDC dimerization. Diaminopimelate decarboxylase (DAPDC)3 (E.C. 4.1.1.20) is a member of the pyridoxal 5Ј-phosphate (PLP)-dependent decarboxylases (1). It catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway of bacteria and plants (2, 3). The product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria. Consequently, DAPDC represents a promising target for the development of novel antibacterial agents (4).A DAPDC reaction mechanism has been previously proposed (5, 6). The reaction mechanism is thought to be initiated by the formation of a Schiff base between PLP and a conserved active site lysine from the (Y/F)AXKA motif (7). The substrate, meso-DAP, then binds and forms a subsequent Schiff base with PLP. This is suggested to be coordinated by the highly conserved CE(S/T)XD motif provided by an adjacent subunit (7). Decarboxylation of meso-DAP is then mediated by the sulfhydryl nucleophile provided by the conserved cysteine of the CE(S/T)XD motif thereby leaving the substrate cradled between two monomers (8). This proposed mechanism suggests DAPDC functions as a dimer.To support this assertion, previous structural studies of DAPDC from Methanocaldococcus jannaschii (PDB codes 1TWI and 1TUF) (9), Aquifex aeolicus (PDB code 2P3E), and Brucella melitensis (PDB code 3VAB) show that the enzyme crystallizes as a homodimer, with each monomer comprised of two domains (9). Domain I forms an ␣/␤ barrel, whereas domain II is comprised of a mixed ␤-sheet flanked by ␣-helices (9). The overall fold is similar to the functionally related enzyme ornithine decarboxylase, which also uses PLP as a cofactor in a decarboxylatio...

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“…Although monomeric (5,17), dimeric (6,7,9), and tetrameric (8) assemblies have been observed in crystal structures of prokaryotic orthologs of DAPDC, the quaternary structure has not yet been investigated for any plant orthologs. To address this, the quaternary structure of the two At-DAPDC enzymes were characterized by analytical ultracentrifugation.…”

Section: At-dapdc Enzymes Exist In a Monomer-dimer Equilibriummentioning

confidence: 99%

Structure–function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control

Crowther

Cross

Oliver

et al. 2019

Journal of Biological Chemistry

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Edited by Joseph M. Jez meso-Diaminopimelate decarboxylase catalyzes the decarboxylation of meso-diaminopimelate, the final reaction in the diaminopimelate L-lysine biosynthetic pathway. It is the only known pyridoxal-5-phosphate-dependent decarboxylase that catalyzes the removal of a carboxyl group from a D-stereocenter. Currently, only prokaryotic orthologs have been kinetically and structurally characterized. Here, using complementation and kinetic analyses of enzymes recombinantly expressed in Escherichia coli, we have functionally tested two putative eukaryotic meso-diaminopimelate decarboxylase isoforms from the plant species Arabidopsis thaliana. We confirm they are both functional meso-diaminopimelate decarboxylases, although with lower activities than those previously reported for bacterial orthologs. We also report in-depth X-ray crystallographic structural analyses of each isoform at 1.9 and 2.4 Å resolution. We have captured the enzyme structure of one isoform in an asymmetric configuration, with one ligand-bound monomer and the other in an apo-form. Analytical ultracentrifugation and smallangle X-ray scattering solution studies reveal that A. thaliana meso-diaminopimelate decarboxylase adopts a homodimeric assembly. On the basis of our structural analyses, we suggest a mechanism whereby molecular interactions within the active site transduce conformational changes to the active-site loop. These conformational differences are likely to influence catalytic activity in a way that could allow for D-stereocenter selectivity of the substrate meso-diaminopimelate to facilitate the synthesis of L-lysine. In summary, the A. thaliana gene loci At3g14390 and At5g11880 encode functional. meso-diaminopimelate decarboxylase enzymes whose structures provide clues to the stereochemical control of the decarboxylation reaction catalyzed by these eukaryotic proteins cro ARTICLE

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Crystallization of diaminopimelate decarboxylase fromEscherichia coli, a stereospecificD-amino-acid decarboxylase

Cited by 12 publications

References 23 publications

Pyridoxal 5-Phosphate Enzymes as Targets for Therapeutic Agents

Pyridoxal 5-Phosphate Enzymes as Targets for Therapeutic Agents

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

Structure–function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control

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