Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes.
D-Cysteine differs from the antiarthritis drug D-penicillamine by only two methyl groups on the beta-carbon yet inhibits carboxypeptidase A (CPD) by a distinct mechanism: D-cysteine binds tightly to the active site zinc, while D-penicillamine catalyzes metal removal. To investigate the structural basis for this difference, we solved the crystal structure of carboxypeptidase A complexed with D-cysteine (D-Cys) at 1.75-A resolution. D-Cys binds the active site zinc with a sulfur ligand and forms additional interactions with surrounding side chains of the enzyme. The structure explains the difference in potency between D-Cys and L-Cys and provides insight into the mechanism of D-penicillamine inhibition. D-Cys binding induces a concerted motion of the side chains around the zinc ion, similar to that found in other carboxypeptidase-inhibitor crystal structures and along a limited path. Analysis of concerted motions of CPD and CPD-inhibitor crystal structures reveals a clustering of these structures into distinct groups. Using the restricted conformational flexibility of a drug target in this type of analysis could greatly enhance efficiency in drug design.
van Aalten
D M
DM
W. M. Keck Structural Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Chong
C R
CR
Joshua-Tor
L
L
D001665:Binding Sites; D002268:Carboxypeptidases / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D043422:Carboxypeptidases A; D003461:Crystallography; D003545:Cysteine / Q000737:chemistry*; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry; D008667:Metalloproteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009038:Motion; D010396:Penicillamine / Q000378:metabolism; D013237:Stereoisomerism; D015032:Zinc / Q000378:metabolism*
D004791:Enzyme Inhibitors; D008667:Metalloproteins; D002268:Carboxypeptidases; D043422:Carboxypeptidases A; D010396:Penicillamine; D015032:Zinc; D003545:Cysteine