We have identified and characterized a structurally novel succinyl-CoA synthetase (SCS) from the hyperthermophilic archaeon Thermococcus kodakaraensis. The presence of an SCS completes the metabolic pathway from glutamate to succinate in the Thermococcales, which had not been clarified due to the absence of classical SCS homologs on their genomes. The SCS from T. kodakaraensis (SCSTk) was a heteromeric enzyme (a2ß2) encoded by TK1880 (a subunit) and TK0943 (ß subunit). Although both SCSTk and classical SCSs harbored the five domains present in enzymes of the acyl-CoA synthetase (nucleoside diphosphate-forming) superfamily, the domain order and their distribution among subunits in SCSTk (a subunit: domains 1-2-5, ß subunit: domains 3-4) were distinct to those of classical SCSs (a: 1-2, ß: 3-4-5), and instead resembled the acetyl-CoA synthetases of Pyrococcus furiosus (ACS IPf and ACS IIPf). Comparison of the four Thermococcales genomes revealed that each strain harbored five a and two ß subunit homologs. Sequence similarity suggested that the ß subunit of SCSTk was also a component of the presumed ACS II in T. kodakaraensis (ACSTk). We co-expressed the a/ß genes of SCSTk (TK1880/TK0943) and those encoding ACS IITk (TK0139/TK0943). ACS IITk recognized a broad range of hydrophobic/aromatic acid compounds as in the case of ACS IIPf, while SCSTk displayed a distinct, and relatively strict substrate specificity towards several acids including succinate. This indicated that the a subunits were responsible for the distinct substrate specificities of SCSTk and ACS IITk.