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 P3₂21. The enzyme shows a low sequence identity of 18% with the structurally known L-fuculose-1-­phosphate aldolase that splits a stereoisomer in a similar reaction. Structure analysis was initiated with a single heavy-atom derivative measured to 6 Å resolution. The resulting poor electron density, a self-rotation function and the working hypothesis that both enzymes are C₄ symmetric with envelopes that resemble one another allowed the location of the 20 protomers of the asymmetric unit. The crystal-packing unit was a D₄-symmetric propeller consisting of five D₄-­symmetric octamers around an internal crystallographic twofold axis. Presumably, the propellers associate laterally in layers, which in turn pile up along the 3₂ axis to form the crystal. The non-crystallographic symmetry was used to extend the phases to the 2.7 Å 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.