1EX8

CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH HP4A, THE TWO-SUBSTRATE-MIMICKING INHIBITOR

Summary for 1EX8

• Entry DOI: 10.2210/pdb1ex8/pdb
• Related: 1CBK 1DY3 1EQ0 1EQM 1EQO 1HKA
• Descriptor: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, MAGNESIUM ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: pyrophosphokinase, pyrophosphoryl transfer, folate, hppk, pterin, atp, bisubstrate-mimicking inhibitor, antimicrobial agent, drug design, substrate specificity, active-site architecture, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 18790.62

Authors

Blaszczyk, J.,Ji, X. (deposition date: 2000-05-01, release date: 2001-05-01, Last modification date: 2023-08-30)

Primary citation

Shi, G.,Blaszczyk, J.,Ji, X.,Yan, H.
Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
J.Med.Chem., 44:1364-1371, 2001

PubMed Abstract: 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), leading to the biosynthesis of folate cofactors. Like other enzymes in the folate pathway, HPPK is an ideal target for the development of antimicrobial agents because the enzyme is essential for microorganisms but is absent from human and animals. Three bisubstrate analogues have been synthesized for HPPK and characterized by biochemical and X-ray crystallographic analyses. All three bisubstrate analogues consist of a pterin, an adenosine moiety, and a link composed of 2-4 phosphoryl groups. P(1)-(6-Hydroxymethylpterin)-P(2)-(5'-adenosyl)diphosphate (HP(2)A, 5) shows little affinity and inhibitory activity for E. coli HPPK. P(1)-(6-Hydroxymethylpterin)-P(3)-(5'-adenosyl)triphosphate (HP(3)A, 6) shows moderate affinity and inhibitory activity with K(d) = 4.25 microM in the presence of Mg(2+) and IC(50) = 1.27 microM. P(1)-(6-Hydroxymethylpterin)-P(4)-(5'-adenosyl)tetraphosphate (HP(4)A, 7) shows the highest affinity and inhibitory activity with K(d) = 0.47 microM in the presence of Mg(2+) and IC(50) = 0.44 microM. The affinity of MgHP(4)A for HPPK is approximately 116 and 76 times higher than that of MgADP and 6-hydroxymethylpterin, respectively. The crystal structure of HPPK in complex with 7 (HPPK.MgHP(4)A) has been determined at 1.85 A resolution with a crystallographic R factor of 0.185. The crystal structure shows that 7 occupies both HP- and ATP-binding sites and induces significant conformational changes in HPPK. The biochemical and structural studies of the bisubstrate analogues indicate that the bisubstrate analogue approach can produce more potent inhibitors for HPPK and the minimum length of the link for a bisubstrate analogue is approximately 7 A.

PubMed: 11311059
DOI: 10.1021/jm0004493

Experimental method

X-RAY DIFFRACTION (1.85 Å)