Journal:Acta Cryst D:S2059798319011355
From Proteopedia
Comparison of a retroviral protease crystallized as a monomer and a dimerStanislaw Wosicki, Miroslaw Gilski, Helena Zabranska, Iva Pichova, Mariusz Jaskolski [1] Molecular Tour All presented crystal forms of dimeric M-PMV PR, i.e.: single mutant with the inhibitor (6s1v), triple mutant with the inhibitor (6s1u), and single mutant without inhibitor (6s1w), are isomorphous and different from the crystals of the monomeric protein, despite the fact that one of the present crystals of dimeric M-PMV PR was obtained using nearly identical crystallization conditions as those that yielded the monomeric form. The crystal structures were solved at resolutions of 1.6 Å, 1.9 Å, and 2.0 Å, respectively. uniquely located between the N26 residues. Side chains of the catalytic aspartates from HIV-1 PR are in semi-transparent orange. Dash lines indicate hydrogen bonds. The water molecule is tetraherally coordinated. The side chains of the T27 residues (at the bottom) form H-bonds called the “fireman’s grip”. The inhibitor molecule has been omitted for clarity. without Wat1 molecule (HIV-1, 4hvp). The structures of M-PMV PR contain an , with the G28 N-H groups acting as donors and the side-chain O atoms of the N26 residues acting as acceptors. This water molecule is different from the nucleophilic molecule found in the active site of active aspartic proteases or from the one found at the inhibitor-flap interface of inhibitor complexes of retropepsins. Such a coordination of a water molecule has not been seen in any (retro)pepsin structures before. . A similar pattern can be partially found in HIV-1 PR (5kr1, 1n49). In the apo structure of the protein (6s1w), one of the flaps (long loops gating access to the active site) is curled into the binding pocket and very well defined in the electron density, while the electron density of the other flap loop is invisible. While flap disorder is not surprising in apo structures of reropepsins, the perfect order of the other flap is an unusual feature, confirming again the unusual structural properties of the M-PMV enzyme. Also intriguingly, the tips of all the flap loops in the inhibitor complexes (6s1v, 6s1u) are disordered and not present in the electron density, although their visible stems seem to trace the direction found in inhibitor complexes of other dimeric retropepsins. The C/A mutations (C7A, C106A) have no effect on the M-PMV PR structure. . PDB references: Crystal structure of dimeric M-PMV protease C7A/D26N/C106A mutant in complex with inhibitor 6s1u; Crystal structure of dimeric M-PMV protease D26N mutant in complex with inhibitor 6s1v; Crystal structure of dimeric M-PMV protease D26N mutant 6s1w. References
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