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Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins.

Nagao S, Ueda M, Osuka H, Komori H, Kamikubo H, Kataoka M, Higuchi Y, Hirota S - PLoS ONE (2015)

Bottom Line: The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping.The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins.These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

ABSTRACT
Cytochrome c (cyt c) family proteins, such as horse cyt c, Pseudomonas aeruginosa cytochrome c551 (PA cyt c551), and Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552), have been used as model proteins to study the relationship between the protein structure and folding process. We have shown in the past that horse cyt c forms oligomers by domain swapping its C-terminal helix, perturbing the Met-heme coordination significantly compared to the monomer. HT cyt c552 forms dimers by domain swapping the region containing the N-terminal α-helix and heme, where the heme axial His and Met ligands belong to different protomers. Herein, we show that PA cyt c551 also forms domain-swapped dimers by swapping the region containing the N-terminal α-helix and heme. The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping. The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins. These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

No MeSH data available.


Related in: MedlinePlus

Crystal structures of monomeric and dimeric WT PA cyt c551.(A) Structure of monomeric WT PA cyt c551 (PDB ID: 351C). (B) Structure of dimeric WT PA cyt c551 solved in this study (pink and cyan, PDB ID: 3X39). The two protomers are depicted in pink and cyan, respectively. The hemes, Cys12, Cys15, His16, and Met61 are shown as stick models. The N- and C-termini are labeled as N and C, respectively. The hemes and Thr20–Met22 residues (hinge loop) are depicted in dark and pale colors, respectively. The sulfur atoms of the heme axial Met ligand and heme-linked Cys are shown in yellow, and the nitrogen atoms of the heme axial His ligand are shown in blue.
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pone.0123653.g002: Crystal structures of monomeric and dimeric WT PA cyt c551.(A) Structure of monomeric WT PA cyt c551 (PDB ID: 351C). (B) Structure of dimeric WT PA cyt c551 solved in this study (pink and cyan, PDB ID: 3X39). The two protomers are depicted in pink and cyan, respectively. The hemes, Cys12, Cys15, His16, and Met61 are shown as stick models. The N- and C-termini are labeled as N and C, respectively. The hemes and Thr20–Met22 residues (hinge loop) are depicted in dark and pale colors, respectively. The sulfur atoms of the heme axial Met ligand and heme-linked Cys are shown in yellow, and the nitrogen atoms of the heme axial His ligand are shown in blue.

Mentions: We solved the X-ray crystal structure of dimeric WT PA cyt c551 at 1.5 Å resolution to elucidate its detailed structure (Fig 2). There were two independent cyt c551 molecules with similar tertiary structures in an asymmetric unit of the crystal. Both cyt c551 molecules exhibited domain-swapped structures, where the N-terminal Glu1–Met22 (helix 1 and loop 1) and the heme were relocated from the original position observed in the monomer. The produced vacant area was occupied by Glu1–Asp19 (helix 1 and half of loop 1) from the other cyt c551 molecule. The hinge loop was constructed with only three amino acids; Thr20, Lys21, and Met22 (S4 Fig). Interestingly, the active site structure of the dimer was formed by the same amino acids as that of the monomer, but the heme axial ligands (His and Met) belonged to different protomers (Fig 3). The swapped region (Glu1–Asp19) and active site structure of dimeric PA cyt c551 were similar to those of dimeric HT cyt c552 [18], but different from those of dimeric horse cyt c, in which the Met80–heme iron bond was disrupted [15].


Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins.

Nagao S, Ueda M, Osuka H, Komori H, Kamikubo H, Kataoka M, Higuchi Y, Hirota S - PLoS ONE (2015)

Crystal structures of monomeric and dimeric WT PA cyt c551.(A) Structure of monomeric WT PA cyt c551 (PDB ID: 351C). (B) Structure of dimeric WT PA cyt c551 solved in this study (pink and cyan, PDB ID: 3X39). The two protomers are depicted in pink and cyan, respectively. The hemes, Cys12, Cys15, His16, and Met61 are shown as stick models. The N- and C-termini are labeled as N and C, respectively. The hemes and Thr20–Met22 residues (hinge loop) are depicted in dark and pale colors, respectively. The sulfur atoms of the heme axial Met ligand and heme-linked Cys are shown in yellow, and the nitrogen atoms of the heme axial His ligand are shown in blue.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4390240&req=5

pone.0123653.g002: Crystal structures of monomeric and dimeric WT PA cyt c551.(A) Structure of monomeric WT PA cyt c551 (PDB ID: 351C). (B) Structure of dimeric WT PA cyt c551 solved in this study (pink and cyan, PDB ID: 3X39). The two protomers are depicted in pink and cyan, respectively. The hemes, Cys12, Cys15, His16, and Met61 are shown as stick models. The N- and C-termini are labeled as N and C, respectively. The hemes and Thr20–Met22 residues (hinge loop) are depicted in dark and pale colors, respectively. The sulfur atoms of the heme axial Met ligand and heme-linked Cys are shown in yellow, and the nitrogen atoms of the heme axial His ligand are shown in blue.
Mentions: We solved the X-ray crystal structure of dimeric WT PA cyt c551 at 1.5 Å resolution to elucidate its detailed structure (Fig 2). There were two independent cyt c551 molecules with similar tertiary structures in an asymmetric unit of the crystal. Both cyt c551 molecules exhibited domain-swapped structures, where the N-terminal Glu1–Met22 (helix 1 and loop 1) and the heme were relocated from the original position observed in the monomer. The produced vacant area was occupied by Glu1–Asp19 (helix 1 and half of loop 1) from the other cyt c551 molecule. The hinge loop was constructed with only three amino acids; Thr20, Lys21, and Met22 (S4 Fig). Interestingly, the active site structure of the dimer was formed by the same amino acids as that of the monomer, but the heme axial ligands (His and Met) belonged to different protomers (Fig 3). The swapped region (Glu1–Asp19) and active site structure of dimeric PA cyt c551 were similar to those of dimeric HT cyt c552 [18], but different from those of dimeric horse cyt c, in which the Met80–heme iron bond was disrupted [15].

Bottom Line: The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping.The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins.These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

ABSTRACT
Cytochrome c (cyt c) family proteins, such as horse cyt c, Pseudomonas aeruginosa cytochrome c551 (PA cyt c551), and Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552), have been used as model proteins to study the relationship between the protein structure and folding process. We have shown in the past that horse cyt c forms oligomers by domain swapping its C-terminal helix, perturbing the Met-heme coordination significantly compared to the monomer. HT cyt c552 forms dimers by domain swapping the region containing the N-terminal α-helix and heme, where the heme axial His and Met ligands belong to different protomers. Herein, we show that PA cyt c551 also forms domain-swapped dimers by swapping the region containing the N-terminal α-helix and heme. The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping. The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins. These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

No MeSH data available.


Related in: MedlinePlus