Vertebrate fructose-1,6-bisphosphate aldolase exists as three isozymes (A, B, and C) that demonstrate kinetic properties that are consistent with their physiological role and tissue-specific expression. The isozymes demonstrate specific substrate cleavage efficiencies along with differences in the ability to interact with other proteins; however, it is unknown how these differences are conferred. An alignment of 21 known vertebrate aldolase sequences was used to identify all of the amino acids that are specific to each isozyme, or isozyme-specific residues (ISRs). The location of ISRs on the tertiary and quaternary structures of aldolase reveals that ISRs are found largely on the surface (24 out of 27) and are all outside of hydrogen bonding distance to any active site residue. Moreover, ISRs cluster into two patches on the surface of aldolase with one of these patches, the terminal surface patch, overlapping with the actin-binding site of aldolase A and overlapping an area of higher than average temperature factors derived from the x-ray crystal structures of the isozymes. The other patch, the distal surface patch, comprises an area with a different electrostatic surface potential when comparing isozymes. Despite their location distal to the active site, swapping ISRs between aldolase A and B by multiple site mutagenesis on recombinant expression plasmids is sufficient to convert the kinetic properties of aldolase A to those of aldolase B. This implies that ISRs influence catalysis via changes that alter the structure of the active site from a distance or via changes that alter the interaction of the mobile C-terminal portion with the active site. The methods used in the identification and analysis of ISRs discussed here can be applied to other protein families to reveal functionally relevant residue clusters not accessible by conventional primary sequence alignment methods.Vertebrate fructose-1,6-bisphosphate aldolase is a ubiquitous tetrameric enzyme that catalyzes reactions in the glycolytic, gluconeogenic, and fructose metabolic pathways (1). The enzyme catalyzes the reversible aldol cleavage of Fru 1,6-P 2 1 into two trioses, glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. It also cleaves the structurally related sugar Fru 1-P into glyceraldehyde and dihydroxyacetone phosphate (2, 3).Vertebrate aldolases exist as three or more isozymes with different tissue distributions: aldolase A (expressed predominantly in muscle), aldolase B (expressed predominantly in liver), and aldolase C (expressed predominantly in brain) (1). The sequences of the mammalian isozymes are highly conserved, exhibiting 81% sequence identity between aldolases A and C (4). Aldolase B is slightly more divergent with ϳ70% sequence identity to both aldolases A and C (5). Consistent with this sequence similarity, isozymes A and C exhibit comparable kinetic properties. Aldolases A and C have evolved to perform the glycolytic reaction, Fru 1,6-P 2 cleavage, more efficiently than aldolase B as demonstrated by a 20 -30-fold higher k ...