Conformational change in substrate binding, catalysis and product release: an open and shut case?

GUTTERIDGE, A

doi:10.1016/s0014-5793(04)00364-3

Cited by 13 publications

(13 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These changes are thought to fulfill a number of roles in catalysis: enhanced binding of substrate, correct orientation of catalytic groups, removal of water from the active site, and trapping of intermediates. Loop motion is classified as an enzyme conformational change, where flexible surface loops move to different conformations (1).…”

mentioning

confidence: 99%

A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax

Vandemeulebroucke¹,

Vos²,

Holsbeke

et al. 2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

The nucleoside hydrolase of Trypanosoma vivax hydrolyzes the N-glycosidic bond of purine nucleosides. Structural and kinetic studies on this enzyme have suggested a catalytic role for a flexible loop in the vicinity of the active sites. Here we present the analysis of the role of this flexible loop via the combination of a proline scan of the loop, loop deletion mutagenesis, steady state and pre-steady state analysis, and x-ray crystallography. Our analysis reveals that this loop has an important role in leaving group activation and product release. The catalytic role involves the entire loop and could only be perturbed by deletion of the entire loop and not by single site mutagenesis. We present evidence that the loop closes over the active site during catalysis, thereby ordering a water channel that is involved in leaving group activation. Once chemistry has taken place, the loop dynamics determine the rate of product release.The importance of conformational changes in enzyme catalysis has long been appreciated. These changes are thought to fulfill a number of roles in catalysis: enhanced binding of substrate, correct orientation of catalytic groups, removal of water from the active site, and trapping of intermediates. Loop motion is classified as an enzyme conformational change, where flexible surface loops move to different conformations (1).Flexible loops are also a common feature of the family of nucleoside hydrolases (EC 3.2.2.1) (2). All structures of the nucleoside hydrolases determined until now show two flexible loops in the vicinity of the active sites, which undergo substantial conformational changes upon association of substrates and inhibitors (2). Nucleoside hydrolases (NHs) 4 catalyze the hydrolysis of the N-glycosidic bond of nucleosides, forming ribose and the corresponding base ( Fig. 1) (2). It has been shown that the NH-catalyzed hydrolysis proceeds via a highly dissociative S N 2-type mechanism with an oxocarbenium ion-like transition state (3, 4). A general catalytic mechanism based on three strategies has been proposed: activation of the nucleophilic water molecule, steric and electrostatic stabilization of the oxocarbenium ion, and leaving group (LG) activation by protonation or hydrogen bonding (2).The purine-specific nucleoside hydrolase of Trypanosoma vivax (TvNH) has been very well characterized kinetically and structurally. This allowed us to put forward a detailed catalytic mechanism to accomplish these strategies. An aspartate (Asp 10 ) in the ribose binding pocket acts as a general base to activate the nucleophile water (5). The oxocarbenium ion is stabilized through interactions between the enzyme and all of the hydroxyl groups (6). The third catalytic strategy, LG activation, was thought to be accomplished by a Brönsted acid, which protonates nitrogen-7 (N-7) of the purine base (2, 7-9). However, in TvNH, no obvious proton donor was found. Here, the LG of the substrate is stacked between the two indole side chains of Trp 83 and Trp 260 ( Fig. 2A). A novel catalytic mechanism...

show abstract

mentioning

confidence: 99%

A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax

Vandemeulebroucke¹,

Vos²,

Holsbeke

et al. 2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Gutteridge and Thornton recognized that catalytic residues of enzymes perform slight side chain motions, while the protein backbone shows only marginal adaptation. Major side chain moves mainly occur on protein surface [5]. Najmanovich et al also considered the side chain flexibility of binding sites.…”

Section: Types Of Flexibilitymentioning

confidence: 99%

Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms

Henzler

Rarey

2011

Methods and Principles in Medicinal Chemistry

View full text Add to dashboard Cite

“…Many proteins contain completely or partially unfolded or disordered segments in their native state, but switch to the folded or ordered conformation due to binding with interacting partners (Dunker et al, 2001;Gutteridge and Thornton, 2004;Dyson and Wright, 2005;Tompa et al, 2005). This intrinsic protein plasticity and the reversible disorder-order structural transition coupled to binding can work as a regulatory switch to control certain biological processes (Tompa et al, 2005;Sandhu and Dash, 2006).…”

Section: Introductionmentioning

confidence: 99%

Investigating the disorder–order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation

Zhang

Tan

Chen

et al. 2010

J of Molecular Recognition

View full text Add to dashboard Cite

We have studied the conformational transition of the calmodulin binding domains (CBD) in several calmodulin-binding kinases, in which CBD changes from the disordered state to the ordered state when binding with calmodulin (CaM). Targeted molecular dynamics simulation was used to investigate the binding process of CaM and CBD of CaM-dependent kinase I (CaMKI-CBD). The results show that CaMKI-CBD began to form an alpha-helix and the interaction free energy between CaM and CaMKI-CBD increased once CaM fully encompassed CaMKI-CBD. Two series of CaM/CBD complex systems, including the complexes of CaM with the initially disordered and the final ordered CBD, were constructed to study the interaction using molecular dynamics simulations. Our analyses suggest that the VDW interaction plays a dominant role in CaM/CBD binding and is a key factor in the disorder-order transition of CBD. Additionally, the entropy effect is not in favor of the formation of the CaM/CBD complex, which is consistent with the experimental evidence. Based on the results, it appears that the CBD conformational change from a non-compact extended structure to compact alpha-helix is critical in gaining a favorable VDW interaction and interaction free energy.

show abstract

Conformational change in substrate binding, catalysis and product release: an open and shut case?

Cited by 13 publications

References 11 publications

A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax

A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax

Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms

Investigating the disorder–order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation

Contact Info

Product

Resources

About