This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis, a protein with an active site that is highly similar to the E. coli O157 z5688 D-lyxose isomerase. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses; YdaD may be active against the ketose sugar produced by YdaE and function in providing resistance to oxidative stress through the production of reducing equivalents in the form of NAD(P)H. YdaE forms a cupin-type beta-barrel, with two alpha helices at the N-terminus. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.
Feature 1: metal binding site [ion binding site], 4 residue positions
Conserved feature residue pattern:[QH] H E H
Evidence:
Comment:The four-coordinate metallocenter includes three histidines and one glutamate. However, this structure has two metal ions, one of which is modeled as a zinc, but is more likely to be a manganese, based on optimal configuration
Structure:2Y0O: Bacillus subtilis D-lyxose isomerase binds 2 metals, zinc and antimony; contacts at 4.0A
Jiyao W et al.(2023). "The conserved domain database in 2023.",