Structure of the complex between trypanosomal triosephosphate isomerase and N‐hydroxy‐4‐phosphono‐butanamide: Binding at the active site despite an “open” flexible loop conformation

Abstract

The structure of triosephosphate isomerase from Trypanosoma brucei complexed with the competitive inhibitor N‐hydroxy‐4‐phosphono‐butanamide was determined by X‐ray crystallography to a resolution of 2.84 å. Full occupancy binding of the inhibitor is observed only at one of the active sites of the homodimeric enzyme where the flexible loop is locked in a completely open conformation by crystal contacts. There is evidence that the inhibitor also binds to the second active site of the enzyme, but with low occupancy. The hydroxamyl group of the inhibitor forms hydrogen bonds to the side chains of Asn 11, Lys 13, and His 95, whereas each of its three methylene units is involved in nonpolar interactions with the side chain of the flexible loop residue Ile 172. Interactions between the hydroxamyl and the catalytic base Glu 167 are absent. The binding of this phosphonate inhibitor exhibits three unusual features: (1) the flexible loop is open, in contrast with the binding mode observed in eight other complexes between triosephosphate isomerase and various phosphate and phosphonate compounds; (2) compared with these complexes the present structure reveals a 1.5‐å shift of the anion‐binding site; (3) this is the first phosphonate inhibitor that is not forced by the enzyme into an eclipsed conformation about the P‐CH2 bond. The results are discussed with respect to an ongoing drug design project aimed at the selective inhibition of glycolytic enzymes of T. brucei.

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

“…In fact, this could provide a means for effective product release (DHAP), which is not the rate-limiting step in the conversion of GAP to DHAP [1,14]. Also in conformity with our current findings, there are two crystal structures reported, in which the loop 6 is in open conformation despite the presence of a ligand [1,15,16].…”

Structures ofPlasmodium falciparumtriosephosphate isomerase complexed to substrate analogues: observation of the catalytic loop in the open conformation in the ligand-bound state

“…The transition from the loop-open (unliganded TIM) to the loopclosed (liganded TIM) form involves a large movement (approximately 7.0 A Ê ) of the¯exible loop. The only example of a ligand-bound TIM with an open-loop conformation is that of TrypTIM bound to the competitive inhibitor N-hydroxy-4-phosphonobutanamide (4PBH; Verlinde et al, 1992).…”

Estrutura cristalográfica da enzima triosefosfato isomerase de Bacillus stearothermophilus e desenho racional de drogas contra a doença do sono

“…brucei, como determinado por tecnicas cristalograficas ( Verlinde et al, 1992b Figura 6.2a -Coeficiente de correlac;ao das soluc;oes da func;ao de rotac;ao cruzada atraves do PC-refinamento do programa XPLOR. Coeficiente de correlac;ao da lista de soluc;oes da func;ao de rotac;ao cruzada.…”

“…Nao existe atualmente nenhuma droga disponivel para 0 tratamento OL' "''''~0ruCO da doenya (Eleventh Programme report of the UNDPIWorld BanklWHO). 3 ) e se liga a conforma~ao aberta da estrutura em volta flexivel ( Verlinde et al, 1992b ). Desta forma e possivel analisar a estrutura em volta flexivel na conforma~ao aberta para a modelagem de compostos que venham a se estender ate 0 shio seletivo da TIM de T. brucei usando como base a estrutura deste complexo determinada por Verlinde et al ( 1992b ).…”

“…A subunidade 2, livre para se adaptar aos diferentes tipos de ligantes provavelmente resultou num melhor padrao para a TIM de T hrllcei complexada com urn inibidor na conformac;ao aberta da estrutura em volta flexivel. 0 modelo foi refinado por Verlinde et al ( 1992b ), atingindo urn fator R de 11,5% para 0 intervalo de resuluc;ao de 6,0 a 2,84 A, com boa geometria.…”