Crystal Structure of Carboxypeptidase A Complexed with d-Cysteine at 1.75 Å − Inhibitor-Induced Conformational Changes

• Published in: Biochemistry (Easton) Vol. 39; no. 33; pp. 10082 - 10089
• Main Authors: van Aalten, Daan M. F, Chong, Curtis R, Joshua-Tor, Leemor
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 22.08.2000
• Subjects: Binding Sites; Carboxypeptidases - antagonists & inhibitors; Carboxypeptidases - chemistry; Carboxypeptidases - metabolism; Carboxypeptidases A; Crystallography; Cysteine - chemistry; Drug Design; Enzyme Inhibitors - chemistry; Metalloproteins - antagonists & inhibitors; Metalloproteins - chemistry; Metalloproteins - metabolism; Models, Molecular; Motion; Penicillamine - metabolism; Stereoisomerism; Zinc - metabolism
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi000952h

d-Cysteine differs from the antiarthritis drug d-penicillamine by only two methyl groups on the β-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-Å 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.