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dc.contributor.authorGygli, Gudrun
dc.contributor.authorLucas, Maria F.
dc.contributor.authorGuallar, Victor
dc.contributor.authorvan Berkel, Willhem J.H.
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2017-11-13T14:49:23Z
dc.date.available2017-11-13T14:49:23Z
dc.date.issued2017-10-06
dc.identifier.citationGygli, G. [et al.]. The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths. "PLoS Computational Biology", 6 Octubre 2017, vol. 13, núm. 10.
dc.identifier.issn1553-734X
dc.identifier.urihttp://hdl.handle.net/2117/110493
dc.description.abstractVanillyl alcohol oxidase (VAO) is a homo-octameric flavoenzyme belonging to the VAO/PCMH family. Each VAO subunit consists of two domains, the FAD-binding and the cap domain. VAO catalyses, among other reactions, the two-step conversion of p-creosol (2-methoxy-4-methylphenol) to vanillin (4-hydroxy-3-methoxybenzaldehyde). To elucidate how different ligands enter and exit the secluded active site, Monte Carlo based simulations have been performed. One entry/exit path via the subunit interface and two additional exit paths have been identified for phenolic ligands, all leading to the si side of FAD. We argue that the entry/exit path is the most probable route for these ligands. A fourth path leading to the re side of FAD has been found for the co-ligands dioxygen and hydrogen peroxide. Based on binding energies and on the behaviour of ligands in these four paths, we propose a sequence of events for ligand and co-ligand migration during catalysis. We have also identified two residues, His466 and Tyr503, which could act as concierges of the active site for phenolic ligands, as well as two other residues, Tyr51 and Tyr408, which could act as a gateway to the re side of FAD for dioxygen. Most of the residues in the four paths are also present in VAO’s closest relatives, eugenol oxidase and p-cresol methylhydroxylase. Key path residues show movements in our simulations that correspond well to conformations observed in crystal structures of these enzymes. Preservation of other path residues can be linked to the electron acceptor specificity and oligomerisation state of the three enzymes. This study is the first comprehensive overview of ligand and co-ligand migration in a member of the VAO/PCMH family, and provides a proof of concept for the use of an unbiased method to sample this process.
dc.description.abstractEnzymes are bionanomachines, which speed up chemical reactions in organisms. To understand how they achieve that, we need to study their mechanisms. Computational enzymology can show us what happens in the enzyme’s active site during a reaction. But molecules need first to reach the active site before a reaction can start. The process of substrate entry and product exit to the active site is often neglected when studying enzymes. However, these two events are of fundamental importance to the proper functioning of any enzyme. We are interested in these dynamic processes to complete our understanding of the mode of action of enzymes. In our work, we have studied substrate and product migration in vanillyl alcohol oxidase. This enzyme can produce the flavour vanillin and enantiopure alcohols, but also catalyses other reactions. The named products are of interest to the flavour- and fine-chemical industries.
dc.description.sponsorshipThis work was supported by: FP7-KBBE- 2013-7-613549 http://cordis.europa.eu/ programme/rcn/851_en.html (see INDOX project (http://indoxproject.eu), funding received by: GG MFL VG WJHvB; and CTQ2016-79138-R, http:// www.mineco.gob.es/portal/site/mineco/?lang_ choosen=en, funding received by: MFL VG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
dc.format.extent27 p.
dc.language.isoeng
dc.publisherPublic Library of Science
dc.rightsAttribution-NonCommercial-NoDerivs 4.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/es/
dc.subjectÀrees temàtiques de la UPC::Enginyeria biomèdica
dc.subject.lcshEnzyme activation
dc.subject.lcshOxidoreductases--Analysis
dc.subject.otherVanillyl alcohol oxidase (VAO)
dc.subject.otherEnzymes
dc.subject.otherComputational enzymology
dc.titleThe ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
dc.typeArticle
dc.subject.lemacEnzims
dc.subject.lemacOxidoreductases
dc.identifier.doi10.1371/journal.pcbi.1005787
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005787
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO/PE2013-2016/CTQ2016-79138-R
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/613549/EU/Optimized oxidoreductases for medium and large scale industrial biotransformations/INDOX
local.citation.publicationNamePLoS Computational Biology
local.citation.volume13
local.citation.number10
local.citation.startingPagee1005787
dc.identifier.pmid28985219


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