The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging

The enzyme L-rhamnulose-1-phosphate aldolase catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate and l-lactaldehyde. It is a homotetramer with an M-r of 30 000 per subunit and crystallized in space group P3(2)21. The enzyme shows a low sequence identity of 18% with the structurally known L-fuculose1-phosphate aldolase that splits a stereoisomer in a similar reaction. Structure analysis was initiated with a single heavy-atom derivative measured to 6 Angstrom resolution. The resulting poor electron density, a self-rotation function and the working hypothesis that both enzymes are C-4 symmetric with envelopes that resemble one another allowed the location of the 20 protomers of the asymmetric unit. The crystal-packing unit was a D-4-symmetric propeller consisting of five D-4 symmetric octamers around an internal crystallographic twofold axis. Presumably, the propellers associate laterally in layers, which in turn pile up along the 3(2) axis to form the crystal. The non-crystallographic symmetry was used to extend the phases to the 2.7 Angstrom resolution limit and to establish a refined atomic model of the enzyme. The structure showed that the two enzymes are indeed homologous and that they possess chemically similar active centres.