Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.
Primary Citation of Related Structures: 1OVR, 1OVU, 1OVV
PubMed Abstract:
The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands ...
The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands. Here, we report the di-Mn(II) and di-Co(II) derivatives of variants of this protein. Together with previously solved structures, 23 crystallographically independent four-helix bundle structures of DF1 variants have been determined, which differ in the bound metal ions and size of the active site cavity. For the di-Mn(II) derivatives, as the size of the cavity increases, the number and polarity of exogenous ligands increases. This collection of structures was analyzed to determine the relationship between protein conformation and the geometry of the active site. The primary mode of backbone movement involves a coordinated tilting and sliding of the first helix in the helix-loop-helix motif. Sliding depends on crystal-packing forces, the steric bulk of a critical residue that determines the dimensions of the active site access cavity, and the intermetal distance. Additionally, a torsional motion of the bridging carboxylates modulates the intermetal distance. This analysis provides a critical evaluation of how conformation, flexibility, and active site accessibility affect the geometry and ligand-binding properties of a metal center. The geometric parameters defining the DF structures were compared to natural diiron proteins; DF proteins have a restricted active site cavity, which may have implications for substrate recognition and chemical stability.
Related Citations:
Sliding Helix Induced Change of Coordination Geomet Model Di-Mn(II) Protein Degrado, W.F., Di Costanzo, L., Geremia, S., Lombardi, A., Pavone, V., Randaccio, L. (2003) Angew Chem Int Ed Engl 42: 417
Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate Accessible Carboxylate-Br Dinuclear Metal Center Di Costanzo, L., Wade, H., Geremia, S., Randaccio, L., Pavone, V., Degrado, W.F., Lombardi, A. (2001) J Am Chem Soc 123: 12749
Retrostructural Analysis of Metalloproteins: Application to the Design of a Minimal Model for Diiron Proteins Lombardi, A., Summa, C.M., Geremia, S., Randaccio, L., Pavone, V., Degrado, W.F. (2000) Proc Natl Acad Sci U S A 97: 6298
Organizational Affiliation:
Centre of Excellence in Biocrystallography, Department of Chemical Science, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy. geremia@units.it
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