DB code: S00428

CATH domain : Deoxyribonuclease I; Chain A Catalytic domain
CSA 1ako
M-CSA 1ako
MACiE M0160

CATH domain Related DB codes (homologues) : Deoxyribonuclease I; Chain A S00429 S00430

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P09030 Exodeoxyribonuclease III
Exonuclease III
AP endonuclease VI
NP_416263.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490010.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF03372 (Exo_endo_phos)
[Graphical View]

KEGG enzyme name
exodeoxyribonuclease III
Escherichia coli exonuclease III
E. coli exonuclease III
endoribonuclease III

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P09030 EX3_ECOLI Exonucleolytic cleavage in the 3''- to 5''- direction to yield nucleoside 5''-phosphates. Monomer.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00434 C00001 C00434 C00608
Compound Double-stranded DNA H2O Double-stranded DNA Deoxyribonucleotide
Type nucleic acids H2O nucleic acids nucleotide
ChEBI 15377
PubChem 22247451
1akoA Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1akoA ASP 229;HIS 259 GLU 34(Mg2+ binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
Fig.2c, p.385 2
Fig.3, p.687-688 2
p.1029-1032, Fig.5a

Comments X-ray crystallography (2.6 Angstroms)
Medline ID 95191690
PubMed ID 7885481
Journal Nature
Year 1995
Volume 374
Pages 381-386
Authors Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA
Title Structure and function of the multifunctional DNA-repair enzyme exonuclease III.
Related PDB 1ako
Related UniProtKB
Comments catalysis
Medline ID 97105903
PubMed ID 8948651
Journal Nucleic Acids Res
Year 1996
Volume 24
Pages 4572-4576
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).
Related PDB
Related UniProtKB
Medline ID
PubMed ID 9057832
Journal Eur J Biochem
Year 1997
Volume 243
Pages 684-9
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.
Related PDB
Related UniProtKB
Medline ID
PubMed ID 10962003
Journal J Biol Chem
Year 2000
Volume 275
Pages 37055-61
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.
Related PDB
Related UniProtKB
Medline ID
PubMed ID 11286553
Journal J Mol Biol
Year 2001
Volume 307
Pages 1023-34
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.
Related PDB
Related UniProtKB
Medline ID
PubMed ID 12758078
Journal J Mol Biol
Year 2003
Volume 329
Pages 311-22
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.
Related PDB
Related UniProtKB

This enzyme belongs to the AP/exoA family.
There are various proposed catalytic mechanisms for this enzyme. Whilst the papers [1], [3], [5] proposed one-metal mechanisms, the paper [6] based on its homologue, Ape1, suggested two-metal mechanism.
According to the papers [1] & [3], 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 [3] suggested a slightly different mechanism from the one proposed by [1], 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 [5] 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 [6] 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.

Created Updated
2002-07-01 2009-02-26