3PH2

Structure of the imidazole-adduct of the Phormidium laminosum cytochrome c6 Q51V variant

Summary for 3PH2

• Entry DOI: 10.2210/pdb3ph2/pdb
• Related: 2V08
• Descriptor: Cytochrome c6, HEME C, IMIDAZOLE, ... (4 entities in total)
• Functional Keywords: class i cytochrome c, photosynthesis, cytochrome f, photosystem i, thylakoid
• Biological source: Phormidium laminosum
• Total number of polymer chains: 1
• Total formula weight: 9580.75

Authors

Worrall, J.A.R. (deposition date: 2010-11-03, release date: 2011-02-09, Last modification date: 2024-11-27)

Primary citation

Rajagopal, B.S.,Wilson, M.T.,Bendall, D.S.,Howe, C.J.,Worrall, J.A.
Structural and kinetic studies of imidazole binding to two members of the cytochrome c (6) family reveal an important role for a conserved heme pocket residue.
J.Biol.Inorg.Chem., 16:577-588, 2011

PubMed Abstract: The amino acid at position 51 in the cytochrome c(6) family is responsible for modulating over 100 mV of heme midpoint redox potential. As part of the present work, the X-ray structure of the imidazole adduct of the photosynthetic cytochrome c(6) Q51V variant from Phormidium laminosum has been determined. The structure reveals the axial Met ligand is dissociated from the heme iron but remains inside the heme pocket and the Ω-loop housing the Met ligand is stabilized through polar interactions with the imidazole and heme propionate-6. The latter is possible owing to a 180° rotation of both heme propionates upon imidazole binding. From equilibrium and kinetic studies, a Val residue at position 51 increases the stability of the Fe-S(Met) interaction and also affects the dynamics associated with imidazole binding. In this respect, the k (obs) for imidazole binding to Arabidopsis thaliana cytochrome c(6A), which has a Val at the position equivalent to position 51 in photosynthetic cytochrome c(6), was found to be independent of imidazole concentration, indicating that the binding process is limited by the Met dissociation rate constant (about 1 s(-1)). For the cytochrome c(6) Q51V variant, imidazole binding was suppressed in comparison with the wild-type protein and the V52Q variant of cytochrome c(6A) was found to bind imidazole readily. We conclude that the residue type at position 51/52 in the cytochrome c(6) family is additionally responsible for tuning the stability of the heme iron-Met bond and the dynamic properties of the ferric protein fold associated with endogenous ligand binding.

PubMed: 21267610
DOI: 10.1007/s00775-011-0758-y

Experimental method

X-RAY DIFFRACTION (1.4 Å)