1EQM

CRYSTAL STRUCTURE OF BINARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE WITH ADENOSINE-5'-DIPHOSPHATE

Summary for 1EQM

• Entry DOI: 10.2210/pdb1eqm/pdb
• Related: 1CBK 1DY3 1EQ0 1EQO 1HKA
• Descriptor: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, MAGNESIUM ION, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: pyrophosphokinase, pyrophosphoryl transfer, folate, hppk, pterin, antimicrobial agent, drug design, substrate specificity, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 18513.01

Authors

Xiao, B.,Blaszczyk, J.,Ji, X. (deposition date: 2000-04-05, release date: 2001-04-05, Last modification date: 2023-08-30)

Primary citation

Xiao, B.,Shi, G.,Gao, J.,Blaszczyk, J.,Liu, Q.,Ji, X.,Yan, H.
Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR.
J.Biol.Chem., 276:40274-40281, 2001

PubMed Abstract: The crystal structure of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in complex with MgADP has been determined at 1.5-A resolution with a crystallographic R factor of 0.191. The solution structure of HPPK in complex with Mg(2+) and beta,gamma-methyleneadenosine 5'-triphosphate (MgAMPPCP) has been determined using a simulated annealing protocol with 3,523 experimental NMR restraints. The root mean square deviation of the ensemble of 20 refined conformers that represent the solution structure from the mean coordinate set derived from them is 0.74 +/- 0.26 A for all backbone atoms and 0.49 +/- 0.22 A when residues Pro(14), Pro(44)-Gln(50), and Arg(84)-Pro(91) are excluded. Binding of MgADP causes significant changes in the conformation and dynamical property of three loops of HPPK that are involved in catalysis. A dramatic, unusual conformational change is that loop 3 moves away from the active center significantly with some residues moving by >17 A. The binding of MgADP also stabilizes loop 1 and loop 3 but makes loop 2 more mobile. Very similar conformational and dynamical changes are observed in the NMR solution structure of HPPK.MgAMPPCP. The conformational and dynamical changes may play important roles in both substrate binding and product release in the catalytic cycle.

PubMed: 11546767

Experimental method

X-RAY DIFFRACTION (1.5 Å)