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Loop Conformation and Dynamics of the Escherichia coli HPPK Apo-Enzyme and Its Binary Complex with MgATP

Rong Yang ^*, Matthew C. Lee ^*, Honggao Yan  and Yong Duan 

^* Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan; and Genome Center and Department of Applied Science, University of California, Davis, California

Correspondence: Address reprint requests to Yong Duan, Genome Center and Dept. of Applied Science, University of California, Davis, CA 95616. Tel.: 530-754-7632; Fax: 530-754-9658; E-mail: duan{at}ucdavis.edu.

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.