DB code: S00428

CATH domain	3.60.10.10 : Deoxyribonuclease I; Chain A	Catalytic domain
E.C.	3.1.11.2
CSA	1ako
M-CSA	1ako
MACiE	M0160

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

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P09030	Exodeoxyribonuclease III	Exonuclease III EXO III EC 3.1.11.2 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
E.C.
Compound	Double-stranded DNA	H2O	Double-stranded DNA	Deoxyribonucleotide
Type	nucleic acids	H2O	nucleic acids	nucleotide
ChEBI		15377 15377
PubChem		22247451 962 22247451 962

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
[1]	Fig.2c, p.385	2
[3]	Fig.3, p.687-688	2
[4]	p.37058-37060
[5]	p.317-320
[6]	p.1029-1032, Fig.5a

References
[1]
Resource
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
[2]
Resource
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
[3]
Resource
Comments
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
[4]
Resource
Comments
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
[5]
Resource
Comments
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
[6]
Resource
Comments
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

Comments
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.

Comments

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