1l6g
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Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine
OverviewOverview
The crystal structures of alanine racemase bound with reaction, intermediate analogs, N-(5'-phosphopyridoxyl)-L-alanine (PLP-L-Ala) and, N-(5'-phosphopyridoxyl)-D-alanine (PLP-D-Ala), were determined at 2.0-A, resolution with the crystallographic R factor of 17.2 for PLP-L-Ala and, 16.9 for PLP-D-Ala complexes. They were quite similar not only to each, other but also to the structure of the native pyridoxal 5'-phosphate, (PLP)-form enzyme; root mean square deviations at Calpha among the three, structures were less than 0.28 A. The side chains of the amino acid, residues around the PLP-L-Ala and PLP-D-Ala were virtually superimposable, on each other as well as on those around PLP of the native holoenzyme. The, alpha-hydrogen of the alanine moiety of PLP-L-Ala was located near the OH, of Tyr(265)', whereas that of PLP-D-Ala was near the NZ of Lys(39). These, support the previous findings that Tyr(265)' and Lys(39) are the catalytic, bases removing alpha-hydrogen from L- and D-alanine, respectively. The, prerequisite for this two-base mechanism is that the alpha-proton, abstracted from the substrate is transferred (directly or indirectly), between the NZ of Lys(39) and the OH of Tyr(265'); otherwise the enzyme, reaction stops after a single turnover. Only the carboxylate oxygen atom, of either PLP-Ala enantiomer occurred at a reasonable position that can, mediate the proton transfer; neither the amino acid side chains nor the, water molecules were located in the vicinity. Therefore, we propose a, mechanism of alanine racemase reaction in which the substrate carboxyl, group directly participates in the catalysis by mediating the proton, transfer between the two catalytic bases, Lys(39) and Tyr(265)'. The, results of molecular orbital calculation also support this mechanism.
About this StructureAbout this Structure
1L6G is a Single protein structure of sequence from Geobacillus stearothermophilus with PDD as ligand. Active as Alanine racemase, with EC number 5.1.1.1 Full crystallographic information is available from OCA.
ReferenceReference
Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine., Watanabe A, Yoshimura T, Mikami B, Hayashi H, Kagamiyama H, Esaki N, J Biol Chem. 2002 May 24;277(21):19166-72. Epub 2002 Mar 8. PMID:11886871
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