Stereochemistry of meso-.alpha.,.epsilon.-diaminopimelate decarboxylase reaction: the first evidence for pyridoxal 5'-phosphate dependent decarboxylation with inversion of configuration

Asada, Yasuhiko; Tanizawa, Katsuyuki; Sawada, Seiji; Suzuki, Tetsuya; Misono, Haruo; Soda, Kenji

doi:10.1021/bi00527a022

Cited by 53 publications

(20 citation statements)

References 30 publications

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“…The product will then consist entirely of molecules that are correspondingly deuterated, and is therefore not only chiral but its optical activity will, in all likelihood, be measurable (subject to the sensitivity of the detection instruments). The chirality of the product can then be determined by the classical method of measuring optical activity followed by assignment of configuration by comparison of this activity with that of standards of known configuration (4,12,14). Alternatively, nmr methods can be applied (9,17) in the configurational assignment.…”

Section: Discussionmentioning

confidence: 99%

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The stereochemistry of the enzymic decarboxylation of L-arginine and of L-ornithine

Richards¹,

Spenser²

1982

Can. J. Chem.

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Section: Discussionmentioning

confidence: 99%

“…L-Ornithine (14) in deuterium oxide gave (-)-(l-2H)putrescine dihydrochloride (15), L-(2-2H)ornithine in water gave (+)-(l-2H)putrescine dihydrochloride. The ORD curves of the two samples are shown in Fig.…”

Section: +Nh3 ( * ) -( 2 -2~)~m I T H I N E Monohydrochloridementioning

confidence: 99%

The stereochemistry of the enzymic decarboxylation of L-arginine and of L-ornithine

Richards¹,

Spenser²

1982

Can. J. Chem.

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“…Therefore, amino acid racemase with low substrate specificity probably belongs to the same family of proteins as alanine racemase: a unique family containing only alanine racemase, mammalian ornithine decarboxylase, and meso-␣,⑀-diaminopimelate (DAP) decarboxylase with little similarity to other PLP enzymes (43). We have shown that the decarboxylation of DAP catalyzed by DAP decarboxylase proceeds through inversion of the configuration of the ␣-carbon of DAP (29). This indicates that the enzyme function must be conducted on both sides of the plane of the substrate⅐PLP complex so as to decarboxylate on one side and to introduce a proton on the other side.…”

Section: Stereospecificity Of Amino Acid Racemases For Hydrogen Abstrmentioning

confidence: 99%

Nonstereospecific Transamination Catalyzed by Pyridoxal Phosphate-dependent Amino Acid Racemases of Broad Substrate Specificity

Lim¹,

Yoshimura²,

Kurokawa³

et al. 1998

Journal of Biological Chemistry

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Pyridoxal 5-phosphate-dependent amino acid racemases of broad substrate specificity catalyze transamination as a side reaction. We studied the stereospecificities for hydrogen abstraction from C-4 of the bound pyridoxamine 5-phosphate during transamination from pyridoxamine 5-phosphate to pyruvate catalyzed by three amino acid racemases of broad substrate specificity. When the enzymes were incubated with (4S)-or (4R)-[4-3 H]pyridoxamine 5-phosphate in the presence of pyruvate, tritium was released into the solvent from both pyridoxamine 5-phosphates. Thus, these enzymes abstract a hydrogen nonstereospecifically from C-4 of the coenzyme in contrast to the other pyridoxal 5-phosphate-dependent enzymes so far studied, which catalyze the stereospecific hydrogen removal. Amino acid racemase of broad substrate specificity from Pseudomonas putida produced D-and L-glutamate from ␣-ketoglutarate through the transamination with L-ornithine. Because glutamate does not serve as a substrate for racemization, the enzyme catalyzed the nonstereospecific overall transamination between L-ornithine and ␣-ketoglutarate. The cleavage and formation of the C-H bond at C-4 of the coenzyme and C-2 of the substrate thus occurs nonstereospecifically on both sides of the plane of the coenzyme-substrate complex intermediate. Amino acid racemase of broad substrate specificity is the first example of a pyridoxal enzyme catalyzing nonstereospecific transamination.Although enzymatic racemization of amino acid is apparently simple, consisting of a nonstereospecific rearrangement of the substrate ␣-hydrogen, several different types of amino acid racemases are found in microorganisms. Aspartate racemase (EC 5.1.1.13) (1) and glutamate racemase (EC 5.1.1.3) (2, 3) are independent of cofactors, and one or more cysteinyl residues play an important role in the abstraction of the ␣-hydrogen from the substrate. Phenylalanine racemase (EC 5.1.1.11), which is involved in gramicidin S synthesis, utilizes ATP (4). Alanine racemase (EC 5.1.1.1) in several microorganisms (5), arginine racemase (EC 5.1.1.9) from Pseudomonas graveolens (6), and amino acid racemases of broad substrate specificity (EC 5.1.1.10) of Aeromonas punctata (7), Pseudomonas striata (8), and Pseudomonas putida (9) all depend on pyridoxal 5Ј-phosphate (PLP)1 . Faraci and Walsh (10) proposed a mechanism for alanine racemase that is probably similar to that of other PLP-dependent amino acid racemases. The reaction is initiated by transaldimination. In this step, PLP bound with the active-site lysyl residue through an internal Schiff base (Scheme IA) reacts with a substrate to form an external Schiff base (B). The subsequent ␣-hydrogen abstraction results in the formation of a resonance-stable anionic intermediate (C). If the reprotonation occurs at C-2 of the substrate moiety on the opposite face of the planar intermediate to that where the proton abstraction occurs, an antipodal aldimine is formed (D). The aldimine complex is subsequently hydrolyzed to form isomerized amino acid and regener...

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“…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).…”

mentioning

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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Stereochemistry of meso-.alpha.,.epsilon.-diaminopimelate decarboxylase reaction: the first evidence for pyridoxal 5'-phosphate dependent decarboxylation with inversion of configuration

Cited by 53 publications

References 30 publications

The stereochemistry of the enzymic decarboxylation of L-arginine and of L-ornithine

The stereochemistry of the enzymic decarboxylation of L-arginine and of L-ornithine

Nonstereospecific Transamination Catalyzed by Pyridoxal Phosphate-dependent Amino Acid Racemases of Broad Substrate Specificity

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

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