Coenzyme A (CoASH) replaces glutathione as the major low-molecular weight thiol in Staphylococcus aureus; it is maintained in the reduced state by coenzyme A-disulfide reductase (CoADR), a homodimeric enzyme similar to NADH peroxidase, but containing a novel Cys43-SSCoA redox center. The crystal structure of S. aureus CoADR has been solved using multiwavelength anomalous dispersion data and refined at a resolution of 1.54 Å. The resulting electron density maps define the Cys43-SSCoA disulfide conformation, with Cys43-S γ located at the flavin si-face, 3.2 Å from FAD-C4aF, and the CoAS-moiety lying in an extended conformation within a cleft at the dimer interface. A well-ordered chloride ion is positioned adjacent to the Cys43-SSCoA disulfide and receives a hydrogen bond from Tyr361′-OH of the complementary subunit, suggesting a role for Tyr361′ as an acid-base catalyst during the reduction of CoAS-disulfide. Tyr419′-OH is located 3.2 Å from Tyr361′-OH as well, and based on its conservation in known functional CoADRs, also appears important for activity. Identification of residues involved in recognition of the CoAS-disulfide substrate and in formation and stabilization of the Cys43-SSCoA redox center has allowed development of a CoAS-binding motif. Bioinformatics analyses indicate that CoADR enzymes are broadly distributed in both bacterial and archaeal kingdoms, suggesting an even broader significance for the CoASH/CoAS-disulfide redox system in prokaryotic thiol/ disulfide homeostasis.In contrast to the central role played by the tripeptide thiol glutathione [GSH; (1)] in maintaining thiol/disulfide homeostasis and providing an important line of antioxidant defense in, for example, Escherichia coli, earlier studies clearly indicated the absence of GSH in a number of Bacteria (2,3) and in all Archaea (4,5). Coenzyme A (CoASH) was shown to be the † This work was supported by National Institutes of Health Grant GM-35394 (A.C.), by National Science Foundation Grant , by grants-in-aid from the Ministry of Education, Culture, Sports, Science and Technology (Monbusho), Japan, and the Japan Society for the Promotion of Science (T.T.), and by National Science Foundation Grant MCB-9982727 (P.A.K.). T.C.M. was the recipient of International Fellowship P-99934 from the Japan Society for the Promotion of Science. A.C. was the recipient of Short-Term Invitation Fellowship RC20137002 from the Japan Society for the Promotion of Science. Data for this study were measured at beamline X26C of the National Synchrotron Light Source. (12) subsequently noted that the PNDORs could be subdivided on the basis of mechanistic and sequence-structural information into three groups, with "Group 3" including CoADR, NADH peroxidase (Npx), and NADH oxidase (Nox). Until the identification of CoADR (6), all flavoprotein disulfide reductases were members of PNDOR Groups 1 and 2, and all Group 3 enzymes were specific for either H 2 O 2 or O 2 (→2H 2 O) reduction. CoADR is clearly by sequence a Group 3 PNDOR enzyme (7); it (like Npx and No...