The structure of the motor domain of the yeast minus-end directed kinesin protein Kar3 has been solved with X-ray crystallographic data to 2.3 Å. Like the Kinesin-1 and Ncd proteins, the Kar3 motor contains a central, eight-stranded, mostly parallel beta-sheet which is bounded on each side by three alpha-helices.
The order of the strands in the beta-sheet is beta2, beta1, beta8, beta3, beta7, beta6, beta4, and beta5 (maintaining the nomenclature used for Kinesin-1 and Ncd). Strands beta6 and beta5 are oriented antiparallel to the remaining strands. There is a small three-stranded antiparallel sheet (beta1a, beta1b, beta1c) which is near strand beta2. The Kar3 protein contains a single molecule of MgADP. The active site is similar to the active sites of the myosin proteins as well as the G-proteins. The Mg2+ ion is coordinated by six oxygens: one oxygen from the side chain of Thr481, one from the beta-phosphate of ADP, and four water molecules. A pocket for the adenine ring is formed by the side chains of Phe482, Arg394, and Pro395.
Kar3 exhibits 46% sequence identity with Ncd over the motor domain and, not surprisingly, the two structures are very similar. The central beta-sheet and the alpha-helices are all located in approximately the same location. The largest difference between the two structures occurs at helix alpha4, which in Kar3 is 9 residues longer (>2 turns of the alpha helix). Although there are four disordered residues immediately preceding alpha4, it is clear that the structure of this region differs dramatically between the two proteins. The alpha4 helix and L11 loop follow the switch II element, a region which is involved in conformational changes in the myosins and the G-proteins. Additionally, the L11 loop of Ncd has been proposed to point into the groove between protofilaments on the microtubule. This structural difference may be relevant to the ability of Kar3 to destabilize microtubules. A second structural difference between Kar3 and Ncd occurs at the L9 loop which joins helices alpha3 and alpha3a. In Kar3, this loop is oriented closer to the active site such that residues from L9 can interact with the hydrogen bonding network at the active site. In Ncd and Kinesin-1, residues from this loop are over 7 Å from the nucleotide.
Contributed by Andy Gulick
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Created 23 December 1997 20:00 GMT
Modified 21 March 2007 02:30 GMT