Background: ATP is the most common phosphoryl group donor for kinases. Howe
ver, certain hyperthermophilic archaea such as Thermococcus litoralis and P
yrococcus furiosus utilize unusual ADP-dependent glucokinases and phosphofr
uctokinases in their glycolytic pathways. These ADP-dependent kinases are h
omologous to each other but show no sequence similarity to any of the hithe
rto known ATP-dependent enzymes.
Results: We solved the crystal structure at 2.3 Angstrom resolution of an A
DP-dependent glucokinase from T, litoralis (tIGK) complexed with ADP. The o
verall structure can be divided into large and small alpha/beta domains, an
d the ADP molecule is buried in a shallow pocket in the large domain. Unexp
ectedly, the structure was similar to those of two ATP-dependent kinases, r
ibokinase and adenosine kinase. Comparison based on three-dimensional struc
ture revealed that several motifs important both in structure and function
are conserved, and the recognition of the alpha- and beta -phosphate of the
ADP in the tIGK was almost identical with the recognition of the beta- and
gamma -phosphate of ATP in these ATP-dependent kinases.
Conclusions: Noticeable points of our study are the first structure of ADP-
dependent kinase, the structural similarity to members of the ATP-dependent
ribokinase family, its rare nucleotide specificity caused by a shift in nu
cleotide binding position by one phosphate unit, and identification of the
residues that discriminate ADP-and ATP-dependence. The strict conservation
of the binding site for the terminal and adjacent phosphate moieties sugges
ts a common ancestral origin of both the ATP- and ADP-dependent kinases.