2VXN

E65Q-TIM complexed with phosphoglycolohydroxamate at 0.82 A resolution

Summary for 2VXN

• Entry DOI: 10.2210/pdb2vxn/pdb
• Related: 1AMK 1IF2 1N55 1QDS
• Descriptor: TRIOSEPHOSPHATE ISOMERASE, PHOSPHOGLYCOLOHYDROXAMIC ACID, 2-PHOSPHOGLYCOLIC ACID, ... (6 entities in total)
• Functional Keywords: isomerase, fatty acid biosynthesis, transition state analogue, glycolysis, pentose shunt, gluconeogenesis, tim, glycosome, triosephosphate isomerase, enzyme-ligand complex, lipid synthesis, transition state, protonation state
• Biological source: LEISHMANIA MEXICANA
• Total number of polymer chains: 1
• Total formula weight: 28054.83

Authors

Alahuhta, M.,Wierenga, R.K. (deposition date: 2008-07-08, release date: 2009-07-14, Last modification date: 2024-05-01)

Primary citation

Alahuhta, M.,Wierenga, R.K.
Atomic Resolution Crystallography of a Complex of Triosephosphate Isomerase with a Reaction-Intermediate Analog: New Insight in the Proton Transfer Reaction Mechanism
Proteins, 78:1878-, 2010

PubMed Abstract: Enzymes achieve their catalytic proficiency by precisely positioning the substrate and catalytic residues with respect to each other. Atomic resolution crystallography is an excellent tool to study the important details of these geometric active-site features. Here, we have investigated the reaction mechanism of triosephosphate isomerase (TIM) using atomic resolution crystallographic studies at 0.82-A resolution of leishmanial TIM complexed with the well-studied reaction-intermediate analog phosphoglycolohydroxamate (PGH). Remaining unresolved aspects of the reaction mechanism of TIM such as the protonation state of the first reaction intermediate and the properties of the hydrogen-bonding interactions in the active site are being addressed. The hydroxamate moiety of PGH interacts via unusually short hydrogen bonds of its N1-O1 moiety with the carboxylate group of the catalytic glutamate (Glu167), for example, the distance of N1(PGH)-OE2(Glu167) is 2.69 +/- 0.01 A and the distance of O1(PGH)-OE1(Glu167) is 2.60 +/- 0.01 A. Structural comparisons show that the side chain of the catalytic base (Glu167) can move during the reaction cycle in a small cavity, located above the hydroxamate plane. The structure analysis suggests that the hydroxamate moiety of PGH is negatively charged. Therefore, the bound PGH mimics the negatively charged enediolate intermediate, which is formed immediately after the initial proton abstraction from DHAP by the catalytic glutamate. The new findings are discussed in the context of the current knowledge of the TIM reaction mechanism.

PubMed: 20235230
DOI: 10.1002/PROT.22701

Experimental method

X-RAY DIFFRACTION (0.82 Å)