title: Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
abstract: The number of metal ions required for phosphoryl transfer in restriction endonucleases is still an unresolved question in molecular biology. The two Ca(2+) and Mn(2+) ions observed in the pre- and post-reactive complexes of BamHI conform to the classical two-metal ion choreography. We probed the Mg(2+) cofactor positions at the active site of BamHI by molecular dynamics simulations with one and two metal ions present and identified several catalytically relevant sites. These can mark the pathway of a single ion during catalysis, suggesting its critical role, while a regulatory function is proposed for a possible second ion.
authors.affiliation: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1113 Budapest, Hungary.
authors.forename: Letif
authors.initials: L
authors.lastname: Mones
authors.forename: István
authors.initials: I
authors.lastname: Simon
authors.forename: Monika
authors.initials: M
authors.lastname: Fuxreiter
mesh_terms: D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D018360:Crystallography, X-Ray; D015245:Deoxyribonuclease BamHI / Q000737:chemistry* / Q000378:metabolism; D008274:Magnesium / Q000378:metabolism; D008345:Manganese / Q000378:metabolism; D008670:Metals / Q000378:metabolism*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D013329:Structure-Activity Relationship
chemical_list: D008670:Metals; D008345:Manganese; D015245:Deoxyribonuclease BamHI; D008274:Magnesium; D002118:Calcium