Stochastic boundary molecular dynamics simulation of L-ribose in the active site of Actinoplanes missouriensis xylose isomerase and its Val135Asn mutant with improved reaction rate
| Autor: | Johanna Karimäki, Juha Kammonen, Olli Lehtonen, Matti Leisola, Ossi Pastinen, Ossi Turunen, Harri Santa |
|---|---|
| Rok vydání: | 2004 |
| Předmět: |
Xylose isomerase
Stereochemistry Ribose Mutant Biophysics Biochemistry Analytical Chemistry Reaction rate Metal chemistry.chemical_compound Molecular Biology Aldose-Ketose Isomerases Binding Sites biology Molecular Structure Hydrogen bond Active site Substrate (chemistry) Micromonosporaceae chemistry Amino Acid Substitution visual_art Mutation biology.protein visual_art.visual_art_medium |
| Zdroj: | Biochimica et biophysica acta. 1749(1) |
| ISSN: | 0006-3002 |
| Popis: | We used molecular dynamics simulations to study how a non-natural substrate, L-ribose, interacts with the active site of Actinoplanes missouriensis xylose isomerase. The simulations showed that L-ribose does not stay liganded in the active site in the same way as D-xylose, in which the oxygens O2 and O4 are liganded to the metal M1. The oxygen O4 of L-ribose moved away from the metal M1 to an upside down position. Furthermore, the distances of the carbons C1 and C2 of L-ribose to the catalytic metal M2 were higher than in the case of D-xylose. These findings explain the extremely low reaction rate of xylose isomerase with L-ribose. The mutation V135N close to the C5-OH of the substrate increased the reaction efficiency 2- to 4-fold with L-ribose. V135N did not affect the reaction with D-xylose and L-arabinose, whereas the reaction with D-glucose was impaired, probably due to a hydrogen bond between Asn-135 and the substrate. When L-ribose was the substrate, Asn-135 formed a hydrogen bond to Glu-181. As a consequence, O4 of L-ribose stayed liganded to the metal M1 in the V135N mutant in molecular dynamics simulations. This explains the decreased K(m) of the V135N mutant with L-ribose. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|