2H54

Crystal structure of human caspase-1 (Thr388->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

Summary for 2H54

• Entry DOI: 10.2210/pdb2h54/pdb
• Related: 1SC3 2FQQ 2FQR 2FQS 2FQU 2FQV 2H48 2H4W 2H4Y 2H51
• Related PRD ID: PRD_000338
• Descriptor: Caspase-1, N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide, ... (4 entities in total)
• Functional Keywords: allosteric site, dimer interface, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm: P29466 P29466
• Total number of polymer chains: 3
• Total formula weight: 30570.47

Authors

Scheer, J.M.,Wells, J.A.,Romanowski, M.J. (deposition date: 2006-05-25, release date: 2008-03-11, Last modification date: 2024-10-16)

Primary citation

Datta, D.,Scheer, J.M.,Romanowski, M.J.,Wells, J.A.
An allosteric circuit in caspase-1.
J.Mol.Biol., 381:1157-1167, 2008

PubMed Abstract: Structural studies of caspase-1 reveal that the dimeric thiol protease can exist in two states: in an on-state, when the active site is occupied, or in an off-state, when the active site is empty or when the enzyme is bound by a synthetic allosteric ligand at the dimer interface approximately 15 A from the active site. A network of 21 hydrogen bonds from nine side chains connecting the active and allosteric sites change partners when going between the on-state and the off-state. Alanine-scanning mutagenesis of these nine side chains shows that only two of them-Arg286 and Glu390, which form a salt bridge-have major effects, causing 100- to 200-fold reductions in catalytic efficiency (k(cat)/K(m)). Two neighbors, Ser332 and Ser339, have minor effects, causing 4- to 7-fold reductions. A more detailed mutational analysis reveals that the enzyme is especially sensitive to substitutions of the salt bridge: even a homologous R286K substitution causes a 150-fold reduction in k(cat)/K(m). X-ray crystal structures of these variants suggest the importance of both the salt bridge interaction and the coordination of solvent water molecules near the allosteric binding pocket. Thus, only a small subset of side chains from the larger hydrogen bonding network is critical for activity. These form a contiguous set of interactions that run from one active site through the allosteric site at the dimer interface and onto the second active site. This subset constitutes a functional allosteric circuit or "hot wire" that promotes site-to-site coupling.

PubMed: 18590738
DOI: 10.1016/j.jmb.2008.06.040

Experimental method

X-RAY DIFFRACTION (1.8 Å)