TERTIARY STRUCTURES OF CLASS-I UBIQUITIN-CONJUGATING ENZYMES ARE HIGHLY CONSERVED - CRYSTAL-STRUCTURE OF YEAST UBC4

The three-dimensional structure of a yeast ubiquitin-conjugating enzym e, encoded by the Saccharomyces cerevisiae UBC4 gene, has been determi ned at 2.7 angstrom. The structure was solved using molecular replacem ent techniques and refined by simulated annealing to an R-factor of 0. 198. Bond lengths and angles in the molecule have root mean square dev iations from ideal values of 0.018 angstrom and 4.0-degrees, respectiv ely. Ubc4 is an alpha/beta protein with four alpha-helices and a four- stranded antiparallel beta-sheet. The ubiquitin-accepting cysteine is located in a cleft between two loops. Comparison with the recently det ermined structure of a different plant enzyme suggests that class I ub iquitin-conjugating enzymes are highly conserved in their three-dimens ional folding. Except for two extra residues at the N- and the C-termi nus of the plant enzyme, the Calpha atoms of the two enzymes can be su perimposed with a root mean square deviation of only 1.52 A. Greater v ariations are found between the surfaces of the two molecules, as most of the identical residues between the two enzymes are either buried o r clustered on one surface that lies adjacent to the ubiquitin-accepti ng cysteine. We suggest that this conserved surface functions in prote in-protein binding during ubiquitin thiol ester formation.