Cargando…

Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis

Protoporphyrinogen oxidase (PPO) is a critical enzyme across life as the last common step in the synthesis of many metalloporphyrins. The reaction mechanism of PPO was assessed in silico and the unstructured loop near the binding pocket was investigated. The substrate, intermediates, and product wer...

Descripción completa

Detalles Bibliográficos
Autores principales: Barker, Abigail L., Barnes, Hamlin, Dayan, Franck E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764921/
https://www.ncbi.nlm.nih.gov/pubmed/33327448
http://dx.doi.org/10.3390/ijms21249495
_version_ 1783628371439124480
author Barker, Abigail L.
Barnes, Hamlin
Dayan, Franck E.
author_facet Barker, Abigail L.
Barnes, Hamlin
Dayan, Franck E.
author_sort Barker, Abigail L.
collection PubMed
description Protoporphyrinogen oxidase (PPO) is a critical enzyme across life as the last common step in the synthesis of many metalloporphyrins. The reaction mechanism of PPO was assessed in silico and the unstructured loop near the binding pocket was investigated. The substrate, intermediates, and product were docked in the catalytic domain of PPO using a modified Autodock method, introducing flexibility in the macrocycles. Sixteen PPO protein sequences across phyla were aligned and analyzed with Phyre2 and ProteinPredict to study the unstructured loop from residue 204–210 in the H. sapiens structure. Docking of the substrate, intermediates, and product all resulted in negative binding energies, though the substrate had a lower energy than the others by 40%. The α-H of C10 was found to be 1.4 angstroms closer to FAD than the β-H, explaining previous reports of the reaction occurring on the meso face of the substrate. A lack of homology in sequence or length in the unstructured loop indicates a lack of function for the protein reaction. This docking study supports a reaction mechanism proposed previously whereby all hydride abstractions occur on the C10 of the tetrapyrrole followed by tautomeric rearrangement to prepare the intermediate for the next reaction.
format Online
Article
Text
id pubmed-7764921
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-77649212020-12-27 Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis Barker, Abigail L. Barnes, Hamlin Dayan, Franck E. Int J Mol Sci Article Protoporphyrinogen oxidase (PPO) is a critical enzyme across life as the last common step in the synthesis of many metalloporphyrins. The reaction mechanism of PPO was assessed in silico and the unstructured loop near the binding pocket was investigated. The substrate, intermediates, and product were docked in the catalytic domain of PPO using a modified Autodock method, introducing flexibility in the macrocycles. Sixteen PPO protein sequences across phyla were aligned and analyzed with Phyre2 and ProteinPredict to study the unstructured loop from residue 204–210 in the H. sapiens structure. Docking of the substrate, intermediates, and product all resulted in negative binding energies, though the substrate had a lower energy than the others by 40%. The α-H of C10 was found to be 1.4 angstroms closer to FAD than the β-H, explaining previous reports of the reaction occurring on the meso face of the substrate. A lack of homology in sequence or length in the unstructured loop indicates a lack of function for the protein reaction. This docking study supports a reaction mechanism proposed previously whereby all hydride abstractions occur on the C10 of the tetrapyrrole followed by tautomeric rearrangement to prepare the intermediate for the next reaction. MDPI 2020-12-14 /pmc/articles/PMC7764921/ /pubmed/33327448 http://dx.doi.org/10.3390/ijms21249495 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Barker, Abigail L.
Barnes, Hamlin
Dayan, Franck E.
Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis
title Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis
title_full Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis
title_fullStr Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis
title_full_unstemmed Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis
title_short Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis
title_sort conformation of the intermediates in the reaction catalyzed by protoporphyrinogen oxidase: an in silico analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764921/
https://www.ncbi.nlm.nih.gov/pubmed/33327448
http://dx.doi.org/10.3390/ijms21249495
work_keys_str_mv AT barkerabigaill conformationoftheintermediatesinthereactioncatalyzedbyprotoporphyrinogenoxidaseaninsilicoanalysis
AT barneshamlin conformationoftheintermediatesinthereactioncatalyzedbyprotoporphyrinogenoxidaseaninsilicoanalysis
AT dayanfrancke conformationoftheintermediatesinthereactioncatalyzedbyprotoporphyrinogenoxidaseaninsilicoanalysis