Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP.
Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK.MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design.
Yang
Rong
R
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
Lee
Matthew C
MC
Yan
Honggao
H
Duan
Yong
Y
D000255:Adenosine Triphosphate / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D017854:Diphosphotransferases / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D007477:Ions; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013696:Temperature; D013997:Time Factors
D029968:Escherichia coli Proteins; D007477:Ions; D008024:Ligands; D002244:Carbon; D000255:Adenosine Triphosphate; D017854:Diphosphotransferases; C019684:2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase; D008274:Magnesium