Binding Site

Alanine racemase, pyridoxal-phosphate attachment site (IPR020622)

Short name: Ala_racemase_pyridoxalP-BS


Alanine racemase catalyses the pyridoxal-dependent conversion of L-alanine into D-alanine, a key component of bacterial peptidoglycan [PMID: 2197992]. In Escherichia coli and Salmonella typhimurium, there are two alanine racemase isoforms, alr is a biosynthetic form required for cell wall formation; and dadB functions in L-alanine catabolism. By contrast with dadB and alr, both of which are monomeric enzymes, the alanine racemase of Bacillaceae are homodimers. In Pseudomonas putida, a broad-specificity amino acid racemase is structurally and functionally related to alanine racemase. The 3D-structure of the dimeric alanine racemase from Bacillus stearothermophilus has been determined to a resolution of 1.9 A [PMID: 9063881]. Each monomer comprises two domains, with an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal beta-strand domain. In the dimer, the mouth of the alpha/beta barrel of one monomer faces the second domain of the other monomer. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the barrel mouth and is covalently linked via an aldimine linkage to Lys39. Several other residues are involved in anchoring the PLP, for example, Arg219 forms a hydrogen bond with the pyridine nitrogen of the cofactor, which is assumed to influence electron delocalisation in PLP-alanine intermediates; Arg136 donates a hydrogen bond to the phenolic oxygen of PLP, and may be involved in substrate binding and stabilisation of intermediates; and Tyr265' is postulated to be a 2 proton donor to the carbanion intermediate [PMID: 9063881].

This pattern signature contains the lysine residue of alanine racemase that acts as the attachment site for the pyridoxal-phosphate group. The sequence around this residue is highly conserved in all forms of the enzyme.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns