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Evolutionary relationships between heme-binding ferredoxin α + β barrels.

Acharya G, Kaur G, Subramanian S - BMC Bioinformatics (2016)

Bottom Line: We analyze the heme-binding sites in these proteins as well as their barrel topologies.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.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.

View Article: PubMed Central - PubMed

Affiliation: CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

A comparative view of the packing topologies of the ferredoxin α + β barrels. (a-f) Left-side diagrams show a top view of the barrels with β-strands indicated as triangles and α-helices as circles. Right-side diagrams show an opened-up view of the barrel with two ferredoxin-like domains placed side-by-side to show β-strand interactions. Only one pair of interacting β-strands can be seen as the other pair is formed by the peripheral-β-strands. The linear arrangement of the secondary structure elements is shown above the opened-up view, with β-strands indicated as arrows and α-helices as rectangles. Each barrel is constituted of four β-α-β units from two ferredoxin-like domains, colored blue, green, yellow and red. Heme is shown as a black star in all but H. thermophilus siroheme decarboxylase where it is shown as a white dotted-outlined star. N- and C-termini of the protein chains are labeled ‘N’ and ‘C’ in black while those of individual ferredoxin-like domains in barrels with duplicated domains are in pink
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Fig2: A comparative view of the packing topologies of the ferredoxin α + β barrels. (a-f) Left-side diagrams show a top view of the barrels with β-strands indicated as triangles and α-helices as circles. Right-side diagrams show an opened-up view of the barrel with two ferredoxin-like domains placed side-by-side to show β-strand interactions. Only one pair of interacting β-strands can be seen as the other pair is formed by the peripheral-β-strands. The linear arrangement of the secondary structure elements is shown above the opened-up view, with β-strands indicated as arrows and α-helices as rectangles. Each barrel is constituted of four β-α-β units from two ferredoxin-like domains, colored blue, green, yellow and red. Heme is shown as a black star in all but H. thermophilus siroheme decarboxylase where it is shown as a white dotted-outlined star. N- and C-termini of the protein chains are labeled ‘N’ and ‘C’ in black while those of individual ferredoxin-like domains in barrels with duplicated domains are in pink

Mentions: Though two ferredoxin-like domains pack to form a structurally similar α + β barrel in all families, we identify two non-identical packing modes of these domains based on the orientation of the two ferredoxin-like domains with respect to each other within the barrel, which we refer to as Type-1 and Type-2 (Table 1, Fig. 2). This orientation determines which β-strands from the adjacent domains are involved in forming hydrogen bonds to constitute the barrel (Table 1, Fig. 2). In Type-1 packing, the two ferredoxin-like domains are oriented such that the N- and C-termini of both the domains are present on one end of the barrel, while in Type-2, the two ferredoxin-like domains are oriented such that the N- and C-termini of one of them are present along one end of the barrel and the N- and C-termini of the other domain are present on the opposite end (Fig. 2a). Such a packing results in an antiparallel β-strand interaction between the β2 from one ferredoxin-like domain and β4 from the other domain in the Type-1-packing mode (β2↑ β3↓ β1↑ β4↓ β2↑ β3↓ β1↑ β4↓), whereas in the Type-2-packing mode, the β2 strands from each of the ferredoxin-like domains interact with the other (β2↑ β3↓ β1↑ β4↓ β4↑ β1↓ β3↑ β2↓) (Fig. 2f). Type-1-packing mode typified by IsdG-like proteins is observed in a majority of the heme-binding proteins of the ferredoxin α + β barrel superfamily, viz., members of the ABM and Cld/DyP/EfeB/HemQ families. Type-2-packing is mostly confined to the OxdA family members and a group of non-heme-binding ferredoxin α + β barrel proteins typified by the hypothetical protein YqjZ (PDB identifier 2GO8) (Fig. 2b). Interestingly, YqjZ-like proteins (PDB identifiers 2GO8, 2FB0, 4NPO) are members of IsdG-ABM family (PF03992) but with a barrel packing resembling that of OxdA. Thus, we observe two different packing modes even between closely related proteins of the ABM ferredoxin α + β barrel family.Fig. 2


Evolutionary relationships between heme-binding ferredoxin α + β barrels.

Acharya G, Kaur G, Subramanian S - BMC Bioinformatics (2016)

A comparative view of the packing topologies of the ferredoxin α + β barrels. (a-f) Left-side diagrams show a top view of the barrels with β-strands indicated as triangles and α-helices as circles. Right-side diagrams show an opened-up view of the barrel with two ferredoxin-like domains placed side-by-side to show β-strand interactions. Only one pair of interacting β-strands can be seen as the other pair is formed by the peripheral-β-strands. The linear arrangement of the secondary structure elements is shown above the opened-up view, with β-strands indicated as arrows and α-helices as rectangles. Each barrel is constituted of four β-α-β units from two ferredoxin-like domains, colored blue, green, yellow and red. Heme is shown as a black star in all but H. thermophilus siroheme decarboxylase where it is shown as a white dotted-outlined star. N- and C-termini of the protein chains are labeled ‘N’ and ‘C’ in black while those of individual ferredoxin-like domains in barrels with duplicated domains are in pink
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835899&req=5

Fig2: A comparative view of the packing topologies of the ferredoxin α + β barrels. (a-f) Left-side diagrams show a top view of the barrels with β-strands indicated as triangles and α-helices as circles. Right-side diagrams show an opened-up view of the barrel with two ferredoxin-like domains placed side-by-side to show β-strand interactions. Only one pair of interacting β-strands can be seen as the other pair is formed by the peripheral-β-strands. The linear arrangement of the secondary structure elements is shown above the opened-up view, with β-strands indicated as arrows and α-helices as rectangles. Each barrel is constituted of four β-α-β units from two ferredoxin-like domains, colored blue, green, yellow and red. Heme is shown as a black star in all but H. thermophilus siroheme decarboxylase where it is shown as a white dotted-outlined star. N- and C-termini of the protein chains are labeled ‘N’ and ‘C’ in black while those of individual ferredoxin-like domains in barrels with duplicated domains are in pink
Mentions: Though two ferredoxin-like domains pack to form a structurally similar α + β barrel in all families, we identify two non-identical packing modes of these domains based on the orientation of the two ferredoxin-like domains with respect to each other within the barrel, which we refer to as Type-1 and Type-2 (Table 1, Fig. 2). This orientation determines which β-strands from the adjacent domains are involved in forming hydrogen bonds to constitute the barrel (Table 1, Fig. 2). In Type-1 packing, the two ferredoxin-like domains are oriented such that the N- and C-termini of both the domains are present on one end of the barrel, while in Type-2, the two ferredoxin-like domains are oriented such that the N- and C-termini of one of them are present along one end of the barrel and the N- and C-termini of the other domain are present on the opposite end (Fig. 2a). Such a packing results in an antiparallel β-strand interaction between the β2 from one ferredoxin-like domain and β4 from the other domain in the Type-1-packing mode (β2↑ β3↓ β1↑ β4↓ β2↑ β3↓ β1↑ β4↓), whereas in the Type-2-packing mode, the β2 strands from each of the ferredoxin-like domains interact with the other (β2↑ β3↓ β1↑ β4↓ β4↑ β1↓ β3↑ β2↓) (Fig. 2f). Type-1-packing mode typified by IsdG-like proteins is observed in a majority of the heme-binding proteins of the ferredoxin α + β barrel superfamily, viz., members of the ABM and Cld/DyP/EfeB/HemQ families. Type-2-packing is mostly confined to the OxdA family members and a group of non-heme-binding ferredoxin α + β barrel proteins typified by the hypothetical protein YqjZ (PDB identifier 2GO8) (Fig. 2b). Interestingly, YqjZ-like proteins (PDB identifiers 2GO8, 2FB0, 4NPO) are members of IsdG-ABM family (PF03992) but with a barrel packing resembling that of OxdA. Thus, we observe two different packing modes even between closely related proteins of the ABM ferredoxin α + β barrel family.Fig. 2

Bottom Line: We analyze the heme-binding sites in these proteins as well as their barrel topologies.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.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.

View Article: PubMed Central - PubMed

Affiliation: CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus