The stereoisomers of α∈-diaminopimelic acid. 3. Properties and distribution of diaminopimelic acid racemase, an enzyme causing interconversion of the <scp>ll</scp> and <i>meso</i> isomers

Antia, Mani; Hoare, D. S.; Work, Elizabeth

doi:10.1042/bj0650448

Cited by 92 publications

(59 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among the more mechanistically interesting PLP-independent amino acid racemases is the DAP epimerase, which interconverts LL-DAP to meso-DAP (Scheme 1) in the biosynthetic pathway leading from L-aspartate to L-lysine (14,15). Because meso-DAP is a precursor to L-lysine and an essential building block of the peptidoglycan layer of the bacterial cell wall, specific inhibitors of the enzymes in the DAP pathway may lead to a new class of antibiotics (4).…”

mentioning

confidence: 99%

Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target

Pillai

Cherney

Diaper

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

113

View full text Add to dashboard Cite

D-amino acids are much less common than their L-isomers but are widely distributed in most organisms. Many D-amino acids, including those necessary for bacterial cell wall formation, are synthesized from the corresponding L-isomers by ␣-amino acid racemases. The important class of pyridoxal phosphate-independent racemases function by an unusual mechanism whose details have been poorly understood. It has been proposed that the stereoinversion involves two active-site cysteine residues acting in concert as a base (thiolate) and an acid (thiol). Although crystallographic structures of several such enzymes are available, with the exception of the recent structures of glutamate racemase from Bacillus subtilis and of proline racemase from Trypanosoma cruzi, the structures either are of inactive forms (e.g., disulfide) or do not allow unambiguous modeling of the substrates in the active sites. Here, we present the crystal structures of diaminopimelate (DAP) epimerase from Haemophilus influenzae with two different isomers of the irreversible inhibitor and substrate mimic aziridino-DAP at 1.35-and 1.70-Å resolution. These structures permit a detailed description of this pyridoxal 5 -phosphate-independent amino acid racemase active site and delineate the electrostatic interactions that control the exquisite substrate selectivity of DAP epimerase. Moreover, the active site shows how deprotonation of the substrates' nonacidic hydrogen at the ␣-carbon (pKa Ϸ 29) by a seemingly weakly basic cysteine residue (pK a Ϸ 8 -10) is facilitated by interactions with two buried ␣-helices. Bacterial racemases, including glutamate racemase and DAP epimerase, are potential targets for the development of new agents effective against organisms resistant to conventional antibiotics.racemase ͉ stereochemical mechanism T he increase in microbial resistance to conventional antibiotics has rekindled intense interest in new methods of inhibiting bacterial cell wall biosynthesis (1), including blocking formation or utilization of D-amino acids such as D-alanine (2), D-glutamate (3), and meso-diaminopimelic acid (4) present in peptidoglycan (5). The inclusion of D-amino acids in the peptidoglycan layer of the cell wall is thought to provide bacteria with protection from the action of host proteases (2). Glutamate racemase (6, 7) and diaminopimelate (DAP) epimerase (EC 5.1.1.7) (8), as well as aspartate racemase (9) and proline racemase (10, 11), are examples of pyridoxal 5Ј-phosphate (PLP)-independent amino acid racemases that invert the configuration at the ␣-carbon of an amino acid without the use of cofactors, metals, or reducible keto or imino functionalities. The proposed ''two-base'' mechanism (11) for these enzymes involves one active-site cysteine thiolate acting as a base to deprotonate the ␣-carbon, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face (Scheme 1). This process is not trivial, because the pK a of the ␣-proton is Ϸ21 for the fully protonated fo...

show abstract

mentioning

confidence: 99%

Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target

Pillai

Cherney

Diaper

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

113

View full text Add to dashboard Cite

show abstract

“…It is notable that the activities of decarboxylase found in normal dried vegetative cells of B. sphaericus and of S. ureae, are respectively, 10 and 3 times higher than those found in most other bacteria (Antia et al 1957); however, considerably lower quantities were present in the asporogenous variant of B. sphaericus, which also has lysine in its cell wall. Nothing is known of the metabolic determinant which causes the change from a vegetative cell containing lysine in its wall mucopeptides to a spore containing diaminopimelic acid.…”

Section: Discussionmentioning

confidence: 89%

“…Omission of pyridoxal phosphate from the Warburg flasks lowered the decarboxylation rate. There was no decarboxylation reaction with LL-diaminopimelic acid, indicating the absence of diaminopimelic racemase (Antia et al 1957).…”

Section: Sporosarcina Ureaementioning

confidence: 99%

“…The majority of Bacillaceae do not decarboxylate meso-diaminopimelic acid (Antia et al 1957); the known exceptions being Clostridium tetani and Bacillus sphaericus. C .…”

Section: Sporosarcina Ureaementioning

confidence: 99%

“…However, certain of its stereoisomers undergo enzymic reactions resembling those of other amino acids : thus, in many types of bacteria the meso-isomer is decarboxylated to L-lysine (Dewey, Hoare & Work, 1954) and is also racemized to the LL-isomer (Antia, Hoare & Work, 1957); all three isomers can transaminate (Meadow & Work, 1958a) while L-amino acid oxidases of Neurospora and snake venoms oxidize meso-and LL-diaminopimelic acid (Work, 1955). Studies on the decarboxylation of meso-diamino-diaminopimelic acid itself was not present in vegetative cells, but was present in the spores.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Oxidation of meso- , Diaminopimelic Acid by Certain Sporulating Species of Bacteria

Antia

Work

1961

Journal of General Microbiology

View full text Add to dashboard Cite

SUMMARYInvestigations were made of the transformations undergone by the stereoisomers of a,€-diaminopimelic acid in suspensions of acetone-dried organisms of two species of sporulating bacteria, Sporosarcina ureae and Bacillus sphaericus, both of which contain diaminopimelic acid in their spores but not in their vegetative cells. Meso-diaminopimelic acid was rapidly decarboxylated by vegetative organisms of both species; it was also utilized by some other unidentified anaerobic reaction. The vegetative organisms also oxidized meso-diaminopimelic acid with release of ammonia. L-Lysine was oxidized by S . ureae, but not by B. sphaericus. Neither LL-nor DD-diaminopimelic acid was attacked by either organism.Disintegrated spores of Bacillus sphaericus did not oxidize meso-diaminopimelic acid, but decarboxylated it and also utilized it by the unidentified anaerobic reaction. The decarboxylation, but not the oxidation, of diaminopimelic acid by Sporosarcina ureae was greatly stimulated by pyridoxal phosphate; both reactions were inhibited by the same compounds. Study of the oxidation was complicated by the side reactions which occurred with S . ureae, but a simpler system was provided by an asporogenous variant of B. sphaericus which did not decarboxylate diaminopimelic acid without added pyridoxal phosphate. Only one equivalent of ammonia was produced, a small amount of CO, was evolved and two equivalents of oxygen were utilized; no oxidation product was identified. The methods of attacking diaminopimelic acid by these two atypical species are compared and discussed in relation to other species in their respective families.

show abstract

Stereochemical Aspects of Pyridoxal Phosphate Catalysis

Dunathan

1971

Advances in Enzymology - And Related Areas of Molecular Biology

View full text Add to dashboard Cite

The stereoisomers of α∈-diaminopimelic acid. 3. Properties and distribution of diaminopimelic acid racemase, an enzyme causing interconversion of the ll and meso isomers

Abstract: A partially purified preparation of diaminopimelic acid decarboxylase from Aerobacter aerogenes was * Part 1: Jackson (1957).

Cited by 92 publications

References 19 publications

Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target

Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target

Oxidation of meso- , Diaminopimelic Acid by Certain Sporulating Species of Bacteria

Stereochemical Aspects of Pyridoxal Phosphate Catalysis

Contact Info

Product

Resources

About