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The extended metal environments of cytochrome c oxidase structures of the bovine heart mitochondrion and the soil bacterium Paracoccus denitrificans were examined. The metals were found to contain a dicopper center, a copper atom, a calcium, magnesium and two proximal hemes. The mitochondrial structure also includes a bound distant zinc ion. Furthermore, several statistically significant residue clusters were discovered, including a histidine-acidic cluster surrounding the environment of magnesium, the two proximal hemes and copper atom.

Our study of the extended metal environment, particularly of the second shell, focuses in this paper on zinc sites. Key findings include: (i) The second shell of mononuclear zinc centers is generally more polar than hydrophobic and prominently features charged residues engaged in an abundance of hydrogen bonding with histidine ligands. Histidine-acidic or histidine-tyrosine clusters commonly overlap the environment of zinc ions. (ii) Histidine tautomeric metal bonding patterns in ligating zinc ions are mixed. For example, carboxypeptidase A, thermolysin, and sonic hedgehog possess the same ligand group (two histidines, one unibidentate acidic ligand, and a bound water), but their histidine tautomeric geometries markedly differ such that the carboxypeptidase A makes only [N.sup.[Delta]1] contacts, thermolysin makes only [N.sup.[Epsilon]2] contacts, and sonic hedgehog uses one of each. Thus the presence of a similar ligand cohort does not necessarily imply the same topology or function at the active site. (iii) Two close histidine ligands H[X.sub.m]H, m [less than or equal to]5, rarely both coordinate a single metal ion in the [N.sup.[Delta]1] tautomeric conformation, presumably to avoid steric conflicts. Mononuclear zinc sites can be classified into six types depending on the ligand composition and geometry. Implications of the results are discussed in terms of divergent and convergent evolution.

The objectives of this and the following paper are to identify commonalities and disparities of the extended environment of mononuclear metal sites centering on Cu, Fe, Mn, and Zn. The extended environment of a metal site within a protein embodies at least three layers: the metal core, the ligand group, and the second shell, which is defined here to consist of all residues distant less than 3.5 [Angstrom] from some ligand of the metal core. The ligands and second-shell residues can be characterized in terms of polarity, hydrophobicity, secondary structures, solvent accessibility, hydrogen-bonding interactions, and membership in statistically significant residue clusters of different kinds. Findings include the following: (i) Both histidine ligands of type I copper ions exclusively attach the [N.sup.[Delta]1] nitrogen of the histidine imidazole ring to the metal, whereas histidine ligands for all mononuclear iron ions and nearly all type II copper ions are ligated via the [N.sup.[Epsilon]2] nitrogen. By contrast, multinuclear copper centers are coordinated predominantly by histidine [N.sup.[Epsilon]2], whereas diiron histidine contacts are predominantly [N.sup.[Delta]1]. Explanations in terms of steric differences between [N.sup.[Delta]1] and [N.sup.[Epsilon]2] are considered. (ii) Except for blue copper (type I), the second-shell composition favors polar residues. (iii) For blue copper, the second shell generally contains multiple methionine residues, which are elements of a statistically significant histidine-cysteine-methionine cluster. Almost half of the second shell of blue copper consists of solvent-accessible residues, putatively facilitating electron transfer. (iv) Mononuclear copper atoms are never found with acidic carboxylate ligands, whereas single [Mn.sup.2+] ion ligands are predominantly acidic and the second shell tends to be mostly buried. (r) The extended environment of mononuclear Fe sites often is associated with histidine-tyrosine or histidine-acidic clusters.

To maximise the assignment of function of the proteins encoded by a genome and to aid the search for novel drug targets, there is an emerging need for sensitive methods of predicting protein function on a genome-wide basis. GeneAtlas™ is an automated, high-throughput pipeline for the prediction of protein structure and function using sequence similarity detection, homology modelling and fold recognition methods. GeneAtlas is described in detail here. To test GeneAtlas, a 'virtual' genome was used, a subset of PDB structures from the SCOP database, in which the functional relationships are known. GeneAtlas detects additional relationships by building 3D models in comparison with the sequence searching method PSI-BLAST. Functionally related proteins with sequence identity below the twilight zone can be recognised correctly. [ABSTRACT FROM AUTHOR]

Examines the extended metal environment, particularly zinc, in protein structures. Details on the second shell of mononuclear zinc centers; Similarities and dissimilarities of the extended metal environment of zinc metal sites; Roles served by zinc in biological systems; What the principal ligands coordinating zinc ions comprises of; Details on the study.