Cargando…

Evolutionary relationships between heme-binding ferredoxin α + β barrels

BACKGROUND: The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several memb...

Descripción completa

Detalles Bibliográficos
Autores principales: Acharya, Giriraj, Kaur, Gurmeet, Subramanian, Srikrishna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835899/
https://www.ncbi.nlm.nih.gov/pubmed/27089923
http://dx.doi.org/10.1186/s12859-016-1033-6
_version_ 1782427693707427840
author Acharya, Giriraj
Kaur, Gurmeet
Subramanian, Srikrishna
author_facet Acharya, Giriraj
Kaur, Gurmeet
Subramanian, Srikrishna
author_sort Acharya, Giriraj
collection PubMed
description BACKGROUND: The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several members of this superfamily bind heme in order to carry out their functions. RESULTS: We analyze the heme-binding sites in these proteins as well as their barrel topologies. Our comparative structural analysis of these heme-binding barrels reveals two distinct modes of packing of the ferredoxin-like domains to constitute the α + β barrel, which is typified by the Type-1/IsdG-like and Type-2/OxdA-like proteins, respectively. We examine the heme-binding pockets and explore the versatility of the α + β barrels ability to accommodate heme or heme-related moieties, such as siroheme, in at least three different sites, namely, the mode seen in IsdG/OxdA, Cld/DyP/EfeB/HemQ and siroheme decarboxylase barrels. CONCLUSIONS: Our study offers insights into the plausible evolutionary relationships between the two distinct barrel packing topologies and relate the observed heme-binding sites to these topologies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1033-6) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4835899
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-48358992016-04-20 Evolutionary relationships between heme-binding ferredoxin α + β barrels Acharya, Giriraj Kaur, Gurmeet Subramanian, Srikrishna BMC Bioinformatics Research Article BACKGROUND: The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several members of this superfamily bind heme in order to carry out their functions. RESULTS: We analyze the heme-binding sites in these proteins as well as their barrel topologies. Our comparative structural analysis of these heme-binding barrels reveals two distinct modes of packing of the ferredoxin-like domains to constitute the α + β barrel, which is typified by the Type-1/IsdG-like and Type-2/OxdA-like proteins, respectively. We examine the heme-binding pockets and explore the versatility of the α + β barrels ability to accommodate heme or heme-related moieties, such as siroheme, in at least three different sites, namely, the mode seen in IsdG/OxdA, Cld/DyP/EfeB/HemQ and siroheme decarboxylase barrels. CONCLUSIONS: Our study offers insights into the plausible evolutionary relationships between the two distinct barrel packing topologies and relate the observed heme-binding sites to these topologies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1033-6) contains supplementary material, which is available to authorized users. BioMed Central 2016-04-18 /pmc/articles/PMC4835899/ /pubmed/27089923 http://dx.doi.org/10.1186/s12859-016-1033-6 Text en © Acharya et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Acharya, Giriraj
Kaur, Gurmeet
Subramanian, Srikrishna
Evolutionary relationships between heme-binding ferredoxin α + β barrels
title Evolutionary relationships between heme-binding ferredoxin α + β barrels
title_full Evolutionary relationships between heme-binding ferredoxin α + β barrels
title_fullStr Evolutionary relationships between heme-binding ferredoxin α + β barrels
title_full_unstemmed Evolutionary relationships between heme-binding ferredoxin α + β barrels
title_short Evolutionary relationships between heme-binding ferredoxin α + β barrels
title_sort evolutionary relationships between heme-binding ferredoxin α + β barrels
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835899/
https://www.ncbi.nlm.nih.gov/pubmed/27089923
http://dx.doi.org/10.1186/s12859-016-1033-6
work_keys_str_mv AT acharyagiriraj evolutionaryrelationshipsbetweenhemebindingferredoxinabbarrels
AT kaurgurmeet evolutionaryrelationshipsbetweenhemebindingferredoxinabbarrels
AT subramaniansrikrishna evolutionaryrelationshipsbetweenhemebindingferredoxinabbarrels