3P63

Structure of M. laminosus Ferredoxin with a shorter L1,2 loop

Summary for 3P63

• Entry DOI: 10.2210/pdb3p63/pdb
• Related: 1A70 1FRK 1OFF 1QT9 4FXC
• Descriptor: Ferredoxin, FE2/S2 (INORGANIC) CLUSTER (2 entities in total)
• Functional Keywords: ferredoxin, thermostability, beta-grasp fold, redox, fe2s2, concerting the l1, 2 loop into a beta-turn, electron transport
• Biological source: Mastigocladus laminosus (Fischerella sp.)
• Total number of polymer chains: 2
• Total formula weight: 21108.40

Authors

Livnah, O.,Nechushtai, R.,Eisenberg-Domovich, Y.,Michaeli, D. (deposition date: 2010-10-11, release date: 2011-02-09, Last modification date: 2023-11-01)

Primary citation

Nechushtai, R.,Lammert, H.,Michaeli, D.,Eisenberg-Domovich, Y.,Zuris, J.A.,Luca, M.A.,Capraro, D.T.,Fish, A.,Shimshon, O.,Roy, M.,Schug, A.,Whitford, P.C.,Livnah, O.,Onuchic, J.N.,Jennings, P.A.
Allostery in the ferredoxin protein motif does not involve a conformational switch.
Proc.Natl.Acad.Sci.USA, 108:2240-2245, 2011

PubMed Abstract: Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.

PubMed: 21266547
DOI: 10.1073/pnas.1019502108

Experimental method

X-RAY DIFFRACTION (2.3 Å)