PDBsum entry 1ex8

Transferase

PDB id: 1ex8

Contents

Protein chain

158 a.a. *

Ligands

A4P

Metals

_MG

_CL

Waters ×167

* Residue conservation analysis

PDB id:

1ex8

Name:

Transferase

Title:

Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with hp4a, the two-substrate-mimicking inhibitor

Structure:

6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.85Å R-factor: 0.211 R-free: 0.242

Authors:

J.Blaszczyk,X.Ji

Key ref:

G.Shi et al. (2001). Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies. J Med Chem, 44, 1364-1371. PubMed id: 11311059 DOI: 10.1021/jm0004493

Date:

01-May-00 Release date: 01-May-01

Protein chain

P26281  (HPPK_ECOLI) -  2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase from Escherichia coli (strain K12)

Seq: 159 a.a.

Struc: 158 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.6.3 - 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.
• Pathway: Folate Biosynthesis (late stages)
• Reaction: 6-hydroxymethyl-7,8-dihydropterin + ATP = (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H⁺

6-hydroxymethyl-7,8-dihydropterin + ATP (Bound ligand (Het Group name = A4P) matches with 64.58% similarity) = (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H(+)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/jm0004493

J Med Chem 44:1364-1371 (2001)

PubMed id: 11311059

Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.

G.Shi, J.Blaszczyk, X.Ji, H.Yan.

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.