THE CUPREDOXIN FOLD: DEFINITION AND ANALYSIS OF THE COMMON CORE STRUCTURE. Michael E.P. Murphy and Elinor T. Adman. Department of Biological Structure, University of Washington, Box 357742, Seattle, WA 98195-7742.

The cupredoxin fold is found in a family of copper containing proteins that include single domain electron transfer proteins and multi-domain multi-subunit enzymes that catalyze a variety of redox reactions including cytochrome c oxidase, nitrite reductase and the blue oxidase family. A method of multiple coordinate superposition was used to compare the three-dimensional structures of members of this family. Equivalent residues were identified by searching for a minimum of four consecutive residues with a r.m.s. deviation from the average coordinates under a defined cut off. The correctness of the alignment was validated by examining main chain hydrogen bonding patterns. A total of 53 alpha carbons (r.m.s. of 1.3 Å) were identified as being equivalent in 23 cupredoxin domains using a cut off of 2.5 Å. The core structure contains both beta-strands and loop regions. None of the helices present in these structures are conserved. A tree was constructed based on positional similarity of the core residue alpha carbons. This tree shows that domains of the multi-domain enzymes are more closely related between enzymes than domains within a single enzyme. Surprisingly, these relationships are independent of the metal content and function of these domains and suggests that domain duplication and differentiation occurred before functional specialization. The structure based tree agrees well with previously published phylogenetic trees. The sequence identity of the equivalent residues between all 23 domains is 19.5%. Despite this low sequence identity the resulting sequence alignment does contain recognizable patterns which may be of use in identifying other members of the structural family including proteins that do not contain copper.