|Activity||Exonucleolytic cleavage in the 3''- to 5''- direction to yield nucleoside 5''-phosphates.|
|Compound table: links to PDB-related databases & PoSSuM|
|Compound||Double-stranded DNA||H2O||Double-stranded DNA||Deoxyribonucleotide|
|Type||nucleic acids||H2O||nucleic acids||nucleotide|
| || || || || || || || || || || || |
|pdb||Catalytic residues||Cofactor-binding residues|
| || || || || || || || || || |
|1akoA||ASP 229;HIS 259||GLU 34(Mg2+ binding)|
|References for Catalytic Mechanism|
|References||Sections||No. of steps in catalysis|
|Comments||X-ray crystallography (2.6 Angstroms)|
|Authors||Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA|
|Title||Structure and function of the multifunctional DNA-repair enzyme exonuclease III.|
|Journal||Nucleic Acids Res|
|Authors||Shida T., Noda M., Sekiguchi J|
|Title||Cleavage of single-and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI).|
|Journal||Eur J Biochem|
|Authors||Black CB, Cowan JA|
|Title||Inert chromium and cobalt complexes as probes of magnesium-dependent enzymes. Evaluation of the mechanistic role of the essential metal cofactor in Escherichia coli exonuclease III.|
|Journal||J Biol Chem|
|Authors||Whisstock JC, Romero S, Gurung R, Nandurkar H, Ooms LM, Bottomley SP, Mitchell CA|
|Title||The inositol polyphosphate 5-phosphatases and the apurinic/apyrimidinic base excision repair endonucleases share a common mechanism for catalysis.|
|Journal||J Mol Biol|
|Authors||Beernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM 3rd, Rupp B|
|Title||Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism.|
|Journal||J Mol Biol|
|Authors||Lowry DF, Hoyt DW, Khazi FA, Bagu J, Lindsey AG, Wilson DM 3rd|
|Title||Investigation of the role of the histidine-aspartate pair in the human exonuclease III-like abasic endonuclease, Ape1.|
|This enzyme belongs to the AP/exoA family.|
There are various proposed catalytic mechanisms for this enzyme. Whilst the papers , ,  proposed one-metal mechanisms, the paper  based on its homologue, Ape1, suggested two-metal mechanism.
According to the papers  & , His229 acts as a catalytic base, which abstracts a proton from a water molecule, opposite site the O3' atom of the scissile phosphate. The resultant nucleophilic hydroxide ion then attacks the phosphate group, resulting in an inversion of its configuration, as it proceeds through a penta-covalent transition state. The metal ion bound to Glu34 interacts with the negatively charged phosphate group and assists the nucleophilic attack of the hydroxyl, by polarizing the P-O3' bond and stablizing the transition state. The carboxylate of Asp151 may play a role as a catalytic acid, to protonate the O3' leaving group.
The literature  suggested a slightly different mechanism from the one proposed by , in which stabilization of the transition state arises through hydrogen-bonding between the waters of hydration of the metal cofactor and the substrate phosphoryl ester.
The literature  suggested based on its homologue, Ape1, that His-Asp pair does not function as either a catalytic base or metal ligand, but is likely to stabilize the pentavalent transition state.
In contrast, the paper  propsed a two-metal mechanism, in which the second metal bound to the residues corresponding to His259 and Asp151 activates a water molecule to generate an hydroxyl ion. This hydroxyl ion carries out nucleophilic attack on the phosphorous 5' to the nucleotide.