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Crystal structures are known for three members of the bacterial neutral protease
family: thermolysin from Bacillus thermoproteolyticus (TLN), the neutral
protease from Bacillus cereus (NEU), and the elastase of Pseudomonas aeruginosa
(PAE), both in free and ligand-bound forms. Each enzyme consists of an
N-terminal and C-terminal domain with the active site formed at the junction of
the two domains. Comparison of the different molecules reveals that the
structure within each domain is well conserved, but there are substantial
hinge-bending displacements (up to 16 degrees) of one domain relative to the
other. These domain motions can be correlated with the presence or absence of
bound inhibitor, as was previously observed in the specific example of PAE
[Thayer, M.M., Flaherty, K.M., & McKay, D.B. (1991) J. Biol. Chem. 266,
2864-2871]. The binding of inhibitor appears to be associated with a reduction
of the domain hinge-bending angle by 6-14 degrees and a closure of the "jaws" of
the active site cleft by about 2 A. Crystallographic refinement of the structure
of thermolysin suggests that electron density seen in the active site of the
enzyme in the original structure determination probably corresponds to a bound
dipeptide. Thus, the crystal structure appears to correspond to an
enzyme-inhibitor or enzyme-product complex, rather than the free enzyme, as has
previously been assumed.
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