Structures of Escherichia coli CMP kinase alone and in complex with CDP: anew fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity

Background: Nucleoside monophosphate kinases (NMP kinases) catalyze the rev ersible transfer of a phosphoryl group from a nucleoside triphosphate to a nucleoside monophosphate. Among them, cytidine monophosphate kinase from Es cherichia coli has a striking particularity: it is specific for CMP, wherea s in eukaryotes a unique UMP/CMP kinase phosphorylates both CMP and UMP wit h similar efficiency. Results: The crystal structure of the CMP kinase apoenzyme from E. coli was solved by single isomorphous replacement and refined at 1.75 Angstrom reso lution. The structure of the enzyme in complex with CDP was determined at 2 .0 Angstrom resolution. Like other NMP kinases, the protein contains a cent ral parallel beta sheet, the strands of which are connected by alpha hetice s. The enzyme differs from other NMP kinases in the presence of a 40-residu e insert situated in the NMP-binding (NMPbind) domain. This insert contains two domains: one comprising a three-stranded antiparallel beta sheet, the other comprising two alpha helices, Conclusions: Two features of the CMP kinase from E. coli have no equivalent in other NMP kinases of known structure. Firstly, the large NMPbind insert undergoes a CDP-induced rearrangement: its beta-sheet domain moves away fr om the substrate, whereas its helical domain comes closer to it in a motion likely to improve the protection of the active site, Secondly, residues in volved in CDP recognition are conserved in CMP kinases and have no counterp art in other NMP kinases. The structures presented here are the first of a new family of NMP kinases specific for CMP.