nucleotide-binding domain (NBD) of Escherichia coli L-xylulose/3-keto-L-gulonate kinase (EcLyxK) and similar proteins
The subfamily contains a group of uncharacterized proteins with similarity to Escherichia coli L-xylulose/3-keto-L-gulonate kinase (EcLyxK; EC 2.7.1.-/EC 2.7.1.53), Pasteurella multocida L-xylulose kinase (PmLyX, also known as L-xylulokinase; EC 2.7.1.53), and Brucella abortus erythritol kinase (BaEryA; EC 2.7.1.215). EcLyxK catalyzes the phosphorylation of L-xylulose and 3-keto-L-gulonate. It is involved in L-lyxose utilization via xylulose and may also be involved in the utilization of 2,3-diketo-L-gulonate. PmLyX catalyzes the phosphorylation of L-xylulose only. BaEryA catalyzes the phosphorylation of erythritol to D-erythritol-1-phosphate. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain.
Comment:catalytic residues (Asp, Thr, Asp) conserved in the FGGY family
Comment:Two Asp residues probably form a metal cofactor binding site and the second Asp residue acts as a catalytic base.
Comment:It has been proposed that the first Asp coordinates and positions the MgATP, and (in concert with the Mg2+) stabilizes the ADP leaving group during the phospho transfer. The second Asp would act as a general base during catalysis, assisting the removal of a proton from the attacking hydroxyl group. The Thr could stabilize the transition state.
Jiyao W et al.(2023). "The conserved domain database in 2023.",