Enzymology of Bacterial Lysine Biosynthesis

Dogovski, Con; Atkinson, Sarah C.; Dommaraju, Sudhir R.; Downton, Matthew T.; Hor, Lilian; Moore, Stephen; Paxman, Jason J.; Peverelli, Martin G.; Qiu, Theresa Wenli; Reumann, Matthias; Siddiqui, Tanzeela; Taylor, Nicole; Wagner, John; Wubben, Jacinta M.; Perugini, Matthew A.

doi:10.5772/34121

Cited by 29 publications

(51 citation statements)

References 115 publications

(197 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Clearly, these cross-interface interactions are highly important. Interestingly, these interactions are also observed for several other enzymes, including dihydrodipicolinate synthase, which catalyzes the first committed and rate-limiting step in the DAP biosynthesis pathway (2,3). For dihydrodipicolinate synthase, dimerization has been shown to be important for completing the active site of each monomer through the interdigitation of a key catalytic triad residue (18,20,22,23,35,40).…”

Section: Discussionmentioning

confidence: 96%

“…Diaminopimelate decarboxylase (DAPDC) 3 (E.C. 4.1.1.20) is a member of the pyridoxal 5Ј-phosphate (PLP)-dependent decarboxylases (1).…”

mentioning

confidence: 99%

“…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.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

Peverelli

Costa

Kirby

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

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...

show abstract

Section: Discussionmentioning

confidence: 96%

“…Diaminopimelate decarboxylase (DAPDC) 3 (E.C. 4.1.1.20) is a member of the pyridoxal 5Ј-phosphate (PLP)-dependent decarboxylases (1).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

Peverelli

Costa

Kirby

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…In bacteria, the pathway yields two metabolites important to bacterial survival (Kobayashi et al, 2003), namely meso-diaminopimelate (meso-DAP) and lysine. meso-DAP is a key component of the peptidoglycan layer in the bacterial cell wall and lysine is a fundamental building block of housekeeping proteins and bacterial virulence factors (Schleifer & Kandler, 1972;Dogovski et al, 2009Dogovski et al, , 2012. As a consequence, enzymes of the DAP pathway are promising antibiotic targets (Hutton et al, 2007;Dogovski et al, 2009Dogovski et al, , 2012.…”

Section: Introductionmentioning

confidence: 99%

“…Dihydrodipicolinate synthase (DHDPS) functions as a key enzyme in the diaminopimelate (DAP) pathway of bacteria, plants and some fungi (Hutton et al, 2007;Dogovski et al, 2009Dogovski et al, , 2012. In bacteria, the pathway yields two metabolites important to bacterial survival (Kobayashi et al, 2003), namely meso-diaminopimelate (meso-DAP) and lysine.…”

Section: Introductionmentioning

confidence: 99%

Cloning to crystallization of dihydrodipicolinate synthase from the intracellular pathogenLegionella pneumophila

et al. 2013

Self Cite

View full text Add to dashboard Cite

Dihydrodipicolinate synthase (DHDPS) catalyses the rate-limiting step in the biosynthesis of meso-diaminopimelate and lysine. Here, the cloning, expression, purification and crystallization of DHDPS from the intracellular pathogen Legionella pneumophila are described. Crystals grown in the presence of highmolecular-weight PEG precipitant and magnesium chloride were found to diffract beyond 1.65 Å resolution. The crystal lattice belonged to the hexagonal space group P6 1 22, with unit-cell parameters a = b = 89.31, c = 290.18 Å , and contained two molecules in the asymmetric unit. The crystal structure was determined by molecular replacement using a single chain of Pseudomonas aeruginosa DHDPS as the search model.

show abstract

Mis‐annotations of a promising antibiotic target in high‐priority gram‐negative pathogens

Impey

Hawkins

et al. 2020

FEBS Letters

View full text Add to dashboard Cite

The rise of antibiotic resistance combined with the lack of new products entering the market has led to bacterial infections becoming one of the biggest threats to global health. Therefore, there is an urgent need to identify novel antibiotic targets, such as dihydrodipicolinate synthase (DHDPS), an enzyme involved in the production of essential metabolites in cell wall and protein synthesis. Here, we utilised a 7‐residue sequence motif to identify mis‐annotation of multiple DHDPS genes in the high‐priority Gram‐negative bacteria Acinetobacter baumannii and Klebsiella pneumoniae. We subsequently confirmed these mis‐annotations using a combination of enzyme kinetics and X‐ray crystallography. Thus, this study highlights the need to ensure genes encoding promising drug targets, like DHDPS, are annotated correctly, especially for clinically important pathogens.PDB ID6UE0.

show abstract

Enzymology of Bacterial Lysine Biosynthesis

Cited by 29 publications

References 115 publications

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

Cloning to crystallization of dihydrodipicolinate synthase from the intracellular pathogenLegionella pneumophila

Mis‐annotations of a promising antibiotic target in high‐priority gram‐negative pathogens

Contact Info

Product

Resources

About