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Science  06 Apr 2007:
Vol. 316, Issue 5821, pp. 19
DOI: 10.1126/science.316.5821.19c

Recent exponential growth in databases as a consequence of big-science projects such as genome sequencing and structural genomics has, in some environments, credentialed bioinformatic analysts and relegated experimental work to the back-benchers. Nevertheless, the significance of mutations can be hard to predict without actually making the proteins and assessing their behavior.

Kona et al. have taken this approach in trying to understand the role of a Cd2+-binding cysteine in the Escherichia coli enzyme KDO8P synthase in comparison to an asparagine in the Aquifex aeolicus version of the same enzyme. The reaction they catalyze is an aldol condensation of phosphoenolpyruvate and arabinose 5-phosphate. This enzymatic step is a critical one in the bacterial biosynthetic pathway leading to lipopolysaccharides and hence is a potential drug target. A comparison of the structures enabled them to make a series of mutations bridging the metallo- and nonmetallo-KDO8P synthases; follow-up kinetic and structural analyses yielded several insights. The cysteine-coordinated metal fulfills the same function as the asparagine carboxamide in binding and orienting a water molecule for attack on the si side at C2. Even though the metallo- and non-metallo-KDO8P synthases produce the same chemical intermediate, probably via the same reaction pathway, the binding constants of the substrates and products differ, which may reflect an evolutionary adaptation to changes in metabolite concentrations. — GJC

Biochemistry 46, 10.1021/bi6024879 (2007).

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