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...
Autores principales: | , , |
---|---|
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 |