Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • apa.csl
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Computational study of the initial step in the mechanism of dehaloperoxidase A: Determination of the protonation scheme at the active site and the movement of the His55 residue
Universidad de la Republic, URY.
Universidad de la Republic, URY.ORCID iD: 0000-0002-6711-4972
Universidad de la Republic, URY.
2015 (English)In: Quantum Modeling of Complex Molecular Systems / [ed] Rivail JL., Ruiz-Lopez M., Assfeld X, Springer , 2015, Vol. 21, p. 367-382Chapter in book (Refereed)
Abstract [en]

Dehalopeoxidase A (DHP A) is a detoxifying enzyme found in the marine worm Amphitrite ornata. This enzyme converts halophenols found in the environment where the worm lives, into quinones by dehalogenation. The enzyme has globin structure and function, but works also as a peroxidase in the presence of H2O2 which binds to the iron present in the heme group. The initial step in the enzymatic reaction path is the transformation of the heme Fe(III) ion into a ferryl (Fe = O) moiety. A distal histidine, His55, is crucial for this process. His55 can occupy two positions, either in the distal pocket of the active center (“closed”), or exposed to the solvent (“open”). NMR experiments show that His55 moves between those positions in the resting state of the enzyme. For this process to occur it is necessary that a gate, composed of a triad Asn37-Lys36-Lys51 and two carboxylates on the heme group, suffer a conformational change before and after the passage of the histidine. We examined computationally this process at the B3LYP/6-31G(d,p) level, within a PCM simulated aqueous environment. This analysis leads us to propose a correction of the experimental structure of the enzyme determined by X-ray crystallography and offers an explanation for different conformations of the twin carboxylates at the heme group observed in the crystals. This new proposal agrees with the experimentally determined electron density distributions and explains the role of the His55 as a functional hook for the peroxide in the aqueous media.

Place, publisher, year, edition, pages
Springer , 2015. Vol. 21, p. 367-382
Series
Challenges and Advances in Computational Chemistry and Physics ; 21
National Category
Bioinformatics (Computational Biology)
Research subject
Biology
Identifiers
URN: urn:nbn:se:kau:diva-80278DOI: 10.1007/978-3-319-21626-3_14Scopus ID: 2-s2.0-85063142924OAI: oai:DiVA.org:kau-80278DiVA, id: diva2:1468422
Available from: 2020-09-17 Created: 2020-09-17 Last updated: 2022-05-18Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textScopus

Authority records

Saenz Mendez, Patricia

Search in DiVA

By author/editor
Saenz Mendez, Patricia
Bioinformatics (Computational Biology)

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 96 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • apa.csl
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf