Structural comparisons of heme binding proteins

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Abstract
Of the 82 3-dimensionally characterized residues of [Pseudomonas aeruginosa] cytochrome c551, 49 are structurally and topologically equivalent to the globin fold and 41 are equivalent to the cytochrome b5 fold, with a respective root mean square separation of 3.5 and 4.9 .ANG. between equivalenced C.alpha. atoms. The common fold represents a central heme binding core, corresponding to the middle exon of certain globin genes. After superposition of the protein folds, the heme irons are separated by 5.4 and 1.6 .ANG., while their heme normals are inclined by 6.degree. and 32.degree., respectively. The heme face, determined by the asymmetric attachment of the vinyl and propionyl side chains, is directed similarly in all 3 heme proteins. The heme itself is rotated by 72.degree. and 116.degree. about its normal, respectively. The minimum base change per codon for the 3 pairwise comparisons corresponds to the expected value of random sequence comparisons. While all 3 heme proteins might have diverged from a common ancestor, their similarity might have arisen from the requirements of heme binding or the utilization of a particularly stable fold. Known structures within commonly accepted divergent families were superimposed to discriminate better between convergence and divergence. Minimum base changes per codon, number of deletions and insertions, percentage of equivalenced residues, precision of heme superposition, and root mean square separation of equivalenced C.alpha. atoms were tested as measures of evolutionary relationships.

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