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Role of Protein Conformational Dynamics in the Catalysis by 6-Hydroxymethyl-7, 8-Dihydropterin Pyrophosphokinase

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Abstract:

Enzymatic catalysis has conflicting structural requirements of the enzyme. In order for the enzyme to form a Michaelis complex, the enzyme must be in an open conformation so that the substrate can get into its active center. On the other hand, in order to maximize the stabilization of the transition state of the enzymatic reaction, the enzyme must be in a closed conformation to maximize its interactions with the transition state. The conflicting structural requirements can be resolved by a flexible active center that can sample both open and closed conformational states. For a bisubstrate enzyme, the Michaelis complex consists of two substrates in addition to the enzyme. The enzyme must remain flexible upon the binding of the first substrate so that the second substrate can get into the active center. The active center is fully assembled and stabilized only when both substrates bind to the enzyme. However, the side-chain positions of the catalytic residues in the Michaelis complex are still not optimally aligned for the stabilization of the transition state, which lasts only approximately 10-13 s. The instantaneous and optimal alignment of catalytic groups for the transition state stabilization requires a dynamic enzyme, not an enzyme which undergoes a large scale of movements but an enzyme which permits at least a small scale of adjustment of catalytic group positions. This review will summarize the structure, catalytic mechanism, and dynamic properties of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase and examine the role of protein conformational dynamics in the catalysis of a bisubstrate enzymatic reaction.





Keywords: 15N relaxation; 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase; AMPCPP; ARGININE 82 AND ARGININE 92; ARGININE 82 AND ARGININE 93; Bisubstrate enzyme; DHFS; DHNA; HP analogue; HPPK; MgATP binding; Michaelis complex; NMR; PDB code; X-ray crystallography; apo enzyme; bisubstrate enzyme; de novo; dihydrofolate reductase; enzymatic catalysi; enzymatic catalysis; enzyme-substrate complex; fluorometry; folate biosynthesis; ligand-bound; protein dynamics; protein's hydrophobic core; ternary complex

Document Type: Research Article

DOI: https://doi.org/10.2174/092986611794654003

Publication date: 2011-04-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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