Premium
ATP conformations and ion binding modes in the active site of anthrax edema factor: A computational analysis
Author(s) -
Martínez Leandro,
Laine Elodie,
Malliavin Thérèse E.,
Nilges Michael,
Blondel Arnaud
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22523
Subject(s) - anthrax toxin , chemistry , active site , binding site , adenylyl cyclase , substrate (aquarium) , crystallography , protein structure , ion , allosteric regulation , adenosine triphosphate , molecular dynamics , biophysics , catalysis , stereochemistry , enzyme , computational chemistry , biochemistry , biology , ecology , organic chemistry , fusion protein , gene , recombinant dna
Abstract The Edema Factor (EF), one of the virulence factors of anthrax, is an adenylyl cyclase that promotes the overproduction of cyclic‐AMP (cAMP) from ATP, and therefore perturbs cell signaling. Crystallographic structures of EF bound to ATP analogs and reaction products, cyclic‐AMP, and Pyrophosphate (PPi), revealed different substrate conformations and catalytic‐cation binding modes, one or two cations being observed in the active site. To shed light into the biological significance of these crystallographic structures, the energetics, geometry, and dynamics of the active site are analyzed using molecular dynamics simulations. The ATP conformation observed in the one‐metal‐ion structure allows stronger interactions with the catalytic ion, and ATP is more restrained than in the structure containing two Mg 2+ ions. Therefore, we propose that the conformation observed in the one‐ion crystal structure is a more probable starting point for the reaction. The simulations also suggest that a C3′‐endo sugar pucker facilitates nucleophilic attack. Additionally, the two‐cation binding mode restrains the mobility of the reaction products, and thus their tendency to dissociate. Proteins 2009. © 2009 Wiley‐Liss, Inc.