In silico approach to understand structure/function relationship of exopolyphosphatase from Escherichia coli

BOETSCH, C; VERGARA-JAQUE, A; LISA, AT; BEASSONI, PR

Termas de Chillan, Chile

Congreso; The first international conference on Bioinformatics SOIBIO 2010; 2010

Sociedad Iberoamericana de Bioinformatica

E. coli exopolyphosphatase (PPX) hydrolyze polyphosphate (PPn) in a procesive way to yield PPn-1  and orthophosphate.PPX is a head to tail dimer and each monomer is divided in an N-terminal domain which posses the catalytic activity and the C-terminal domain, which is involved in the binding of long chain of PPn [1]. E121 is the putative catalytic residue, and residues D143 G145, S148 and E150 are proposed to form the Mg2+binding pocket [2]. Is not very clear the interaction with long chains of PPn. Alvarado et al. and Rangarajan et al [2, 3] describe a putative region to bind long chain of PPn based on sulfate ions present in the crystal and based on the electrostatic potential.In this work, we performed molecular simulation with PPX bound to Mg+2 and docking assays with small chain PPn (PP3 and PP5) and organic ligands (Guanosine, Adenosine ATP, ADP, ppGpp and pppGpp).Our docking results showed that all ligands can bind in the vicinity of the catalytic site, pointing the terminal phosphate to the catalytic residue E121. pppGpp also interacts with K42, K221 and R267and PP5 besides has close contact with positive and polar residues.Electrostatic potential calculations performed with APBS, suggest that PPn would bind in the dimer interface and also around the active site. This is in agreement with the fact that C-terminal domain is necessary for binding of long chain PPn [1].