Functionally important carboxyl groups in glucoamylase G2 from Aspergillus niger were identified using a differential labelling approach which involved modification of the acarbose-inhibited enzyme with 1-ethyl-3-(4-azonia-4,4-dimethylpentyl)carbodiimide (EAC) and inactivation by [3H]EAC following removal of acarbose.Subsequent sequence localization of the substituted acidic residues was facilitated by specific phenylthiohydantoins. The acid cluster Asp176, Glu179 and Glu180 reacted exclusively with [3H]EAC, while Aspl 12, Asp153, Glu259 and Glu389 had incorporated both [3H]EAC and EAC. It is conceivable that one or two of the [3H]EAC-labelled side chains act in catalysis while the other fully protected residue(s) participates in substrate binding probably together with the partially protected ones. Twelve carboxyl groups that reacted with EAC in the enzyme-acarbose complex were also identified.Asp176, Glu179 and Glu180 are all invariant in fungal glucoamylases. Glu180 was tentatively identified as a catalytic group on the basis of sequence alignments to catalytic regions in isomaltase and a-amylase. The partially radiolabelled Aspl 12 corresponds in Taka-amylase A to Tyr75 situated in a substrate binding loop at a distance from the site of cleavage. A possible correlation between carbodiimide modification of an essential carboxyl group and its role in the glucoamylase catalysis is discussed.Fungal glucoamylase (EC 3.2.1.3; 1,4-a-glucan glucohydrolase) has a wide application in the industrial production of glucose syrups from starch [l, 21. Functionally important side chains have previously been localized in the enzyme from Aspergillus niger [3 -71 and have guided regional sequence alignment with different starch-and oligosaccharide-degrading enzymes [8, 91. This insight into structure/function relationships in glucoamylases made it possible to produce purposely altered enzymes by site-directed mutagenesis [lo -121.Catalytic carboxyl groups have been identified in crystallographic studies of a-amylases [8,13] and by affinity labelling in P-amylases [14, 151 and isomaltase [16 -181. These residues appear conserved in a-amylase, maltase, cyclodextrin glucanotransferase, isoamylase, pullulanase and maltogenic a-amylase [9, 19 -221 ; structure predictions of maltase and cyclodextrin glucanotransferases further show they contain an %/&barrel domain [19] like the a-amylases [8, 131. Much less similarity could be recognized, however, with glucoamylase, P-amylase and isomaltase [9]; their catalytic groups had to be experimentally identified. It was decided to apply the differential labelling approach to glucoamylase because it had failed to react with potential affinity labelling reagents (G. Legler and Y. Nitta, personal communications).The catalytic site in glucoamylase is believed to consist of two carboxyl groups [23,24]. In accordance with a commonly accepted mechanism for carbohydrases [8, 13, 16, 25 -271, one of these acts as a general acid, protonating the glucosidic oxygen of the scissile bond, while the other...