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The structure of alanine racemase from Acinetobacter baumannii.

Davis E, Scaletti-Hutchinson E, Opel-Reading H, Nakatani Y, Krause KL - Acta Crystallogr F Struct Biol Commun (2014)

Bottom Line: As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target.The substrate entryway and active site of the enzymes were shown to be highly conserved.The structure of AlrAba will provide the template required for future structure-based drug-design studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.

ABSTRACT
Acinetobacter baumannii is an opportunistic Gram-negative bacterium which is a common cause of hospital-acquired infections. Numerous antibiotic-resistant strains exist, emphasizing the need for the development of new antimicrobials. Alanine racemase (Alr) is a pyridoxal 5'-phosphate dependent enzyme that is responsible for racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target. The crystal structure of A. baumannii alanine racemase (AlrAba) from the highly antibiotic-resistant NCTC13302 strain has been solved to 1.9 Å resolution. Comparison of AlrAba with alanine racemases from closely related bacteria demonstrates a conserved overall fold. The substrate entryway and active site of the enzymes were shown to be highly conserved. The structure of AlrAba will provide the template required for future structure-based drug-design studies.

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Active site of A. baumannii alanine racemase. (a) 2Fo− Fc electron-density map of the active site contoured at 1.0σ with isomesh map shown (1.6 Å carve). The main-chain and side-chain atoms of the AlrAba active-site residues are depicted as sticks. C atoms are green, O atoms red, N atoms blue, S atoms yellow and phosphates orange. The PLP cofactor is depicted as a ball-and-stick model in which C atoms are coloured black. (b) Superposition of the active-site residues of alanine racemases from A. baumannii (green), B. henselae (blue), P. aeruginosa (red) and E. coli (orange). For A. baumannii, a hybrid view is depicted with residues from monomer B, except for the side chain of His159 which is included from monomer A. The PLP cofactors from each structure are depicted as ball-and-stick models. Primes denote residues contributed by the second monomer. The superposition was performed using the residue ranges stated in Table 2 ▶. This figure was produced in PyMOL (DeLano, 2002 ▶).
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fig5: Active site of A. baumannii alanine racemase. (a) 2Fo− Fc electron-density map of the active site contoured at 1.0σ with isomesh map shown (1.6 Å carve). The main-chain and side-chain atoms of the AlrAba active-site residues are depicted as sticks. C atoms are green, O atoms red, N atoms blue, S atoms yellow and phosphates orange. The PLP cofactor is depicted as a ball-and-stick model in which C atoms are coloured black. (b) Superposition of the active-site residues of alanine racemases from A. baumannii (green), B. henselae (blue), P. aeruginosa (red) and E. coli (orange). For A. baumannii, a hybrid view is depicted with residues from monomer B, except for the side chain of His159 which is included from monomer A. The PLP cofactors from each structure are depicted as ball-and-stick models. Primes denote residues contributed by the second monomer. The superposition was performed using the residue ranges stated in Table 2 ▶. This figure was produced in PyMOL (DeLano, 2002 ▶).

Mentions: The active-site residues of AlrAba and other alanine racemases superimpose particularly well, with low r.m.s differences (Table 2 ▶). The active-site structure of AlrAba is most similar to that of DadXPao (0.56 Å; 58% sequence identity). AlrAba also shares high similarity to AlrEco (0.65 Å; 60% sequence identity), but diverges most from AlrBhe (0.91 Å; 48% sequence identity). This indicates a positive correlation between sequence identity and structural similarity in this region. As mentioned in §3.1, the active site of AlrAba is composed of residues from both monomers, several of which are involved in a hydrogen-bond network with the PLP cofactor (Figs. 2 ▶ and 5 ▶a) and are conserved between alanine racemases (Fig. 5 ▶b).


The structure of alanine racemase from Acinetobacter baumannii.

Davis E, Scaletti-Hutchinson E, Opel-Reading H, Nakatani Y, Krause KL - Acta Crystallogr F Struct Biol Commun (2014)

Active site of A. baumannii alanine racemase. (a) 2Fo− Fc electron-density map of the active site contoured at 1.0σ with isomesh map shown (1.6 Å carve). The main-chain and side-chain atoms of the AlrAba active-site residues are depicted as sticks. C atoms are green, O atoms red, N atoms blue, S atoms yellow and phosphates orange. The PLP cofactor is depicted as a ball-and-stick model in which C atoms are coloured black. (b) Superposition of the active-site residues of alanine racemases from A. baumannii (green), B. henselae (blue), P. aeruginosa (red) and E. coli (orange). For A. baumannii, a hybrid view is depicted with residues from monomer B, except for the side chain of His159 which is included from monomer A. The PLP cofactors from each structure are depicted as ball-and-stick models. Primes denote residues contributed by the second monomer. The superposition was performed using the residue ranges stated in Table 2 ▶. This figure was produced in PyMOL (DeLano, 2002 ▶).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4157418&req=5

fig5: Active site of A. baumannii alanine racemase. (a) 2Fo− Fc electron-density map of the active site contoured at 1.0σ with isomesh map shown (1.6 Å carve). The main-chain and side-chain atoms of the AlrAba active-site residues are depicted as sticks. C atoms are green, O atoms red, N atoms blue, S atoms yellow and phosphates orange. The PLP cofactor is depicted as a ball-and-stick model in which C atoms are coloured black. (b) Superposition of the active-site residues of alanine racemases from A. baumannii (green), B. henselae (blue), P. aeruginosa (red) and E. coli (orange). For A. baumannii, a hybrid view is depicted with residues from monomer B, except for the side chain of His159 which is included from monomer A. The PLP cofactors from each structure are depicted as ball-and-stick models. Primes denote residues contributed by the second monomer. The superposition was performed using the residue ranges stated in Table 2 ▶. This figure was produced in PyMOL (DeLano, 2002 ▶).
Mentions: The active-site residues of AlrAba and other alanine racemases superimpose particularly well, with low r.m.s differences (Table 2 ▶). The active-site structure of AlrAba is most similar to that of DadXPao (0.56 Å; 58% sequence identity). AlrAba also shares high similarity to AlrEco (0.65 Å; 60% sequence identity), but diverges most from AlrBhe (0.91 Å; 48% sequence identity). This indicates a positive correlation between sequence identity and structural similarity in this region. As mentioned in §3.1, the active site of AlrAba is composed of residues from both monomers, several of which are involved in a hydrogen-bond network with the PLP cofactor (Figs. 2 ▶ and 5 ▶a) and are conserved between alanine racemases (Fig. 5 ▶b).

Bottom Line: As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target.The substrate entryway and active site of the enzymes were shown to be highly conserved.The structure of AlrAba will provide the template required for future structure-based drug-design studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.

ABSTRACT
Acinetobacter baumannii is an opportunistic Gram-negative bacterium which is a common cause of hospital-acquired infections. Numerous antibiotic-resistant strains exist, emphasizing the need for the development of new antimicrobials. Alanine racemase (Alr) is a pyridoxal 5'-phosphate dependent enzyme that is responsible for racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target. The crystal structure of A. baumannii alanine racemase (AlrAba) from the highly antibiotic-resistant NCTC13302 strain has been solved to 1.9 Å resolution. Comparison of AlrAba with alanine racemases from closely related bacteria demonstrates a conserved overall fold. The substrate entryway and active site of the enzymes were shown to be highly conserved. The structure of AlrAba will provide the template required for future structure-based drug-design studies.

Show MeSH
Related in: MedlinePlus