Eukaryotic DNA topoisomerase I (Top1) is a monomeric protein clamp that functions in DNA replication, transcription, and recombination. Opposable ''lip'' domains form a salt bridge to complete Top1 protein clamping of duplex DNA. Changes in DNA topology are catalyzed by the formation of a transient phosphotyrosyl linkage between the active-site Tyr-723 and a single DNA strand. Substantial protein domain movements are required for DNA binding, whereas the tight packing of DNA within the covalent Top1-DNA complex necessitates some DNA distortion to allow rotation. To investigate the effects of Top1-clamp closure on enzyme catalysis, molecular modeling was used to design a disulfide bond between residues Gly-365 and Ser-534, to crosslink protein loops more proximal to the active-site tyrosine than the protein loops held by the Lys-369 -Glu-497 salt bridge. In reducing environments, Top1-Clamp was catalytically active. However, contrary to crosslinking the salt-bridge loops [Carey, J. D NA topoisomerases alter DNA topology by the concerted cleavage and religation of DNA strand(s) (reviewed in refs. 1-3). The nucleophilic attack of an active-site tyrosine on a phosphodiester DNA bond generates a phosphotyrosyl linkage, providing a transient protein-linked gate through which another DNA strand or duplex may pass. A second transesterification resolves the tyrosyl-DNA linkage to restore DNA integrity. DNA topoisomerases play critical roles in most DNA transactions, including DNA replication, transcription, and recombination, as well as chromosome segregation. These enzymes also constitute the targets of clinically important anticancer and antibacterial agents (4-6). With human DNA topoisomerase I (Top1), camptothecin (CPT) analogues (topotecan and CPT-11) have shown remarkable antitumor activity against pediatric and adult malignancies (7). These agents poison Top1 by reversibly stabilizing the covalent enzyme-DNA complex, inducing S-phase-dependent cell lethality.Type IB enzymes, including eukaryotic and vaccinia virus Top1, are distinct from other enzymes in that the active-site tyrosine becomes linked to a 3Ј-phosphoryl end, versus the 5Ј-phosphotyrosine bond formed by types IA and II enzymes (1-3). Crystallographic data indicate that the monomeric enzymes (types IA and IB) or the protein subunits that constitute the symmetrical halves of type II enzymes [DNA gyrase and DNA topoisomerase II (Top2)] form a protein clamp (1-3). Yet, type IB enzymes are again unique in that biochemical and structural data support a mechanism of DNA rotation, as opposed to the coordinated domain movements in types IA and II enzymes that are necessary for an enzyme-bridging mechanism (1, 3, 8).The conserved central domain of eukaryotic Top1 forms the protein clamp (Fig. 1). Subdomains I and II constitute the upper cap, which is connected by a flexible hinge to the bottom part of the clamp, subdomain III. Two extended ␣-helices connect the clamp core with the conserved C-terminal domain, containing the activesite tyrosine. Human Top1 struc...