3gwq

Protein Summary

Gene Bxe_A4060 from Burkholderia xenovorans lb400 translates into the YP_556991 protein, a member of the alanine racemase N-term domain group (PF01168). YP_556991 protein is likely a bacterial homolog of the yeast D-serine dehydratase YGL196W.

3gwq crystallizes as a dimer. It contains a TIM fold at the middle part (53-287) from the PLP-binding barrel superfamily, Ala racemase-like N-terminal domain fmaily. The N-terminal region is involved in dimerization, and the C-terminal sequence folds into a separate domain, located near the dimer interface. A search by DALI using 3gwq as query returns as top hits the BTRK protein 2j66 (Z=23), the diaminopimelate decarboxylase 3c5q (Z=23), and the Ala racemase 1vfs (Z=22). The active site in the TIM domain (near H76) bears similarity to 1njj (Z=22), but is not highly conserved. The closest structural matches to 3gwq found by SSM include: 1njj, 3c5q, 2qgh.

It is likely that 3gwq is an enzyme that functions in D-amino acid metabolism, and binds PLP, based on gene neighborhood and the structure similarity of the middle section with 1xfc (Z=21). However, the active site differs significantly, except for Lys78 and Arg275. As a result, further analysis is needed to understand the function of this protein.

Figure 1: 3gwq monomer

Figure 2: 3gwq dimer

To do: try co-xtallization with PLP.

Ligand Summary