Structural basis of heme binding in the Cu,Zn superoxide dismutase from Haemophilus ducreyi.
The Cu,Zn superoxide dismutase from Haemophilus ducreyi is characterized by the unique ability to bind heme at its dimer interface. Here we report the high-resolution crystal structures of this protein in the heme-loaded (holo) and heme-free (apo) forms. Heme is asymmetrically bound between the two enzyme subunits, where heme iron is coordinated by two histidine residues, His64 and His 124, provided by the two subunits. Moreover, the binding of heme to the protein is ensured by stabilizing contacts between the prosthetic group and a limited number of other residues, most of which are not present in other bacterial enzyme variants. We show that the introduction of only three mutations at the dimer interface of the enzyme from Haemophilus parainfluenzae, a closely related bacterial species, is sufficient to induce heme-binding ability by this enzyme variant. Heme binding does not alter protein activity. Moreover, the binding of the prosthetic group does not induce any significant structural perturbation at the subunit level and requires only limited local structural rearrangements that widen the cleft at the dimer interface and cause a limited shift in the relative orientation between the subunits. The presence of a preformed heme-binding pocket and the significant solvent exposure of the cofactor to the solvent are compatible with the suggested protective role of the enzyme against heme toxicity or with its involvement in heme trafficking in the periplasmic space.
Töro
Imre
I
Structural and Computational Biology Programme, EMBL-Heidelberg, Germany.
Petrutz
Cristiana
C
Pacello
Francesca
F
D'Orazio
Melania
M
Battistoni
Andrea
A
Djinović-Carugo
Kristina
K
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D019281:Dimerization; D006191:Haemophilus ducreyi / Q000737:chemistry*; D044135:Haemophilus parainfluenzae / Q000235:genetics / Q000378:metabolism; D006418:Heme / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017354:Point Mutation; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment; D013482:Superoxide Dismutase / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; D006418:Heme; D013482:Superoxide Dismutase