The enzyme consists of one domain with an α/β character.  The domain contains an active site at a β-sheet/α-helix interface, complete with a bound s-mercaptocysteine.  The protein contains a total of 373 residues, and the secondary structure consists of 14 α-helices and 18 β-sheets. 

The active site pocket contains mostly hydrophobic residues, with a handful of polar residues near the back of the site, seeming to slightly surround the back end of the ligand.  The outer shell of the enzyme contains mostly polar groups, and a cross-section of the enzyme reveals a hydrophobic core.  The secondary structure of the shell of the protein consists mainly of α-helical structure, with a few points where β-sheets seem to permeate the surface.  The active site pocket contains an α-helix/β-sheet interface.

Currently, no topology data exists for this enzyme.  However, the structure of this enzyme is very similar to that of the rhodanese-type model of a thiosulfate sulfurtransferase.  The rhodanese enzyme is commonly found in all phyla, and is a well characterized sulfur transferase enzyme. The active site contains a catalytic cysteine (Cys253) with a rhodanese-type fold of β-sheet structure, indicating quite strongly that this is indeed the active site of the enzyme.  A rhodanese-type fold contains a cysteine residue with a tandem repeat system of amino acids. An inhibitory sulfite molecule also exists at arginine residues 74 and 185.

A proposed method of catalysis for the 3-mercaptopyruvate sulfurtransferase enzyme states that the carbonyl group may be polarized by Ser255 in order to assist the thiophilic attack described previously in the reaction scheme, while the two arginine residues previously mentioned (74 and 185) bind to the carboxylate group.  This model is supported through the sensitivity of Ser255 to introduction of a serine protease inhibitor, which consequently lowers the activity of the enzyme.