RESUMEN
Eukaryotic Cu,Zn superoxide dismutases (CuZnSODs) are antioxidant enzymes remarkable for their unusually stable beta-barrel fold and dimer assembly, diffusion-limited catalysis, and electrostatic guidance of their free radical substrate. Point mutations of CuZnSOD cause the fatal human neurodegenerative disease amyotrophic lateral sclerosis. We determined and analyzed the first crystallographic structure (to our knowledge) for CuZnSOD from a prokaryote, Photobacterium leiognathi, a luminescent symbiont of Leiognathid fish. This structure, exemplifying prokaryotic CuZnSODs, shares the active-site ligand geometry and the topology of the Greek key beta-barrel common to the eukaryotic CuZnSODs. However, the beta-barrel elements recruited to form the dimer interface, the strategy used to forge the channel for electrostatic recognition of superoxide radical, and the connectivity of the intrasubunit disulfide bond in P. leiognathi CuZnSOD are discrete and strikingly dissimilar from those highly conserved in eukaryotic CuZnSODs. This new CuZnSOD structure broadens our understanding of structural features necessary and sufficient for CuZnSOD activity, highlights a hitherto unrecognized adaptability of the Greek key beta-barrel building block in evolution, and reveals that prokaryotic and eukaryotic enzymes diverged from one primordial CuZnSOD and then converged to distinct dimeric enzymes with electrostatic substrate guidance.
Asunto(s)
Photobacterium/enzimología , Pliegue de Proteína , Estructura Secundaria de Proteína , Superóxido Dismutasa/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , Rastreo Diferencial de Calorimetría , Bovinos , Clonación Molecular , Secuencia Conservada , Cristalografía por Rayos X , Dimerización , Escherichia coli , Peces/microbiología , Haemophilus/enzimología , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Homología de Secuencia de Aminoácido , Superóxido Dismutasa/biosíntesis , Superóxido Dismutasa/aislamiento & purificaciónRESUMEN
The active site Cu ion in Cu,Zn superoxide dismutase is alternately oxidized and reduced during the enzymatic dismutation of superoxide to hydrogen peroxide and molecular oxygen. For oxidized Cu,Zn superoxide dismutase, an atomic structure has been determined for the human enzyme at 2.5 A resolution. The resolution of the bovine enzyme structure has been extended to 1.8 A. Atomic resolution data has been collected for reduced and inhibitor-bound Cu,Zn superoxide dismutases, and the interpretation of the electron density difference maps is in progress. The geometry and molecular surfaces of the active sites in these structures, together with biochemical data, suggest a specific model for the enzyme mechanism. Similarities in the active site geometry of the Mn and Fe superoxide dismutases with the Cu,Zn enzyme suggest that dismutation in these enzymes may follow a similar mechanism.
Asunto(s)
Superóxido Dismutasa/química , Animales , Sitios de Unión , Bovinos , Cobre , Espectroscopía de Resonancia por Spin del Electrón , Humanos , Hierro , Espectroscopía de Resonancia Magnética , Manganeso , Modelos Moleculares , Estructura Molecular , Oxidación-Reducción , Conformación Proteica , Relación Estructura-Actividad , Superóxido Dismutasa/antagonistas & inhibidores , Superóxido Dismutasa/metabolismo , Superóxidos/metabolismo , Difracción de Rayos X , ZincRESUMEN
In principle, protein thermostability depends on efficient interior packing of apolar residues and on avoidance of irreversible denaturation in the unfolded state. To study these effects, the single free cysteine in the highly stable enzyme bovine Cu,Zn superoxide dismutase was mutated to alanine (Cys6----Ala), and the recombinant protein was expressed in yeast, purified, characterized for reversible and irreversible denaturation, crystallized isomorphously to the wild-type enzyme, and used to determine the atomic structure. Removal of the chemically reactive thiol significantly decreased the rate of irreversible denaturation (as monitored by thermal inactivation at 70 degrees C), but the observed energetic cost (delta delta G of 0.7-1.3 kcal/mol as determined by differential scanning calorimetry) was much less than predicted from either the change in hydrophobicity or packing due to removal of the interior sulfur atom. X-ray diffraction data were collected to 2.1-A resolution using an area detector, and the atomic model for the mutant enzyme was determined by fitting to electron density difference maps, followed by reciprocal space refinement both with stereochemical restraints using PROLSQ and with molecular dynamics using X-PLOR. The refined 2.1-A resolution crystallographic structure suggests that small concerted and compensating shifts (less than 0.5 A) of the surrounding side chains and of the adjacent N- and C-terminal beta-strands significantly reduced the energetic cost of the interior mutation by improving packing and stereochemistry in the mutant enzyme. Taken together, these results differentiate between the effects of reversible and irreversible processes as they impact the design of thermostable proteins and suggest that relatively subtle concerted shifts can significantly reduce the energetic cost of evolutionary variation in internal residues of proteins with Greek key beta-barrel folds.
Asunto(s)
Cisteína , Superóxido Dismutasa/genética , Alanina , Secuencia de Aminoácidos , Animales , Rastreo Diferencial de Calorimetría , Bovinos , Cristalización , Estabilidad de Enzimas , Calor , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Mutación , Conformación Proteica , Superóxido Dismutasa/metabolismo , Difracción de Rayos XRESUMEN
The dimeric high spin c-type cytochrome c' from Chromatium vinosum has been crystallized and the crystals characterized by x-ray diffraction. This cytochrome c' exhibits ligand-controlled dissociation from a dimer to a monomer upon binding carbon monoxide and represents an opportunity to obtain unique information concerning cooperativity in heme proteins. The C. vinosum cytochrome c' protein crystals are grown from polyethylene glycol 4000 and grow in both space group P2(1)2(1)2(1) (a = 49.2, b = 56.7, c = 98.8 A) and space group P2(1) (a = 55, b = 94, c = 50, beta = 106.1 A) depending upon the growth rate, with the P2(1)2(1)2(1) form favored at slower growth rates. The high resolution (2.0 A) atomic structure of the P2(1)2(1)2(1) form is being determined.
Asunto(s)
Chromatium/análisis , Grupo Citocromo c , Monóxido de Carbono/metabolismo , Cristalización , Grupo Citocromo c/metabolismo , Sustancias Macromoleculares , Difracción de Rayos XRESUMEN
Crystals of a copper-zinc superoxide dismutase from Photobacterium leiognathi, a luminescent marine bacterium that is the species-specific symbiont of the ponyfish, have been obtained from 2-methyl-2,4-pentanediol solutions. The space group was determined using screenless small-angle precession photographs, and was confirmed by analyzing area detector diffraction data with the XENGEN programs for indexing and refinement. The crystals are monoclinic, space group C2 (a = 126.4 A, b = 87.0 A, c = 44.4 A, beta = 92.8 A), and have two 32,000 Mr dimers per asymmetric unit. The crystals diffract to at least 2.7 A resolution, are resistant to radiation damage, and are suitable for determination of the structure by X-ray diffraction.