EzCatDB: S00428

DB codeS00428
CATH domainDomain 13.60.10.10Catalytic domain
E.C.3.1.11.2
CSA1ako
MACiEM0160

CATH domainRelated DB codes (homologues)
3.60.10.10S00429,S00430

Enzyme Name
Swiss-protKEGG

P09030
Protein nameExodeoxyribonuclease IIIexodeoxyribonuclease III
Escherichia coli exonuclease III
E. coli exonuclease III
endoribonuclease III
SynonymsExonuclease III
EXO III
EC 3.1.11.2
AP endonuclease VI


Swiss-prot:Accession NumberP09030
Entry nameEX3_ECOLI
ActivityExonucleolytic cleavage in the 3''- to 5''- direction to yield nucleoside 5''-phosphates.
SubunitMonomer.
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00434C00001C00434C00608
CompoundDouble-stranded DNAH2ODouble-stranded DNADeoxyribonucleotide
Typenucleic acidsH2Onucleic acidsnucleotide
1akoAUnbound
UnboundUnbound

Active-site residues
pdbCatalytic residuesCofactor-binding residues
1akoAASP 229;HIS 259
GLU 34(Mg2+ binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.2c, p.3852
[3]Fig.3, p.687-6882
[4]p.37058-37060
[5]p.317-320
[6]p.1029-1032, Fig.5a

references
[1]
CommentsX-ray crystallography (2.6 Angstroms)
Medline ID95191690
PubMed ID7885481
JournalNature
Year1995
Volume374
Pages381-386
AuthorsMol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA
TitleStructure and function of the multifunctional DNA-repair enzyme exonuclease III.
Related PDB1ako
[2]
Commentscatalysis
Medline ID97105903
PubMed ID8948651
JournalNucleic Acids Res
Year1996
Volume24
Pages4572-4576
AuthorsShida T., Noda M., Sekiguchi J
TitleCleavage of single-and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI).
[3]
PubMed ID9057832
JournalEur J Biochem
Year1997
Volume243
Pages684-9
AuthorsBlack CB, Cowan JA
TitleInert 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.
[4]
PubMed ID10962003
JournalJ Biol Chem
Year2000
Volume275
Pages37055-61
AuthorsWhisstock JC, Romero S, Gurung R, Nandurkar H, Ooms LM, Bottomley SP, Mitchell CA
TitleThe inositol polyphosphate 5-phosphatases and the apurinic/apyrimidinic base excision repair endonucleases share a common mechanism for catalysis.
[5]
PubMed ID11286553
JournalJ Mol Biol
Year2001
Volume307
Pages1023-34
AuthorsBeernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM 3rd, Rupp B
TitleTwo divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism.
[6]
PubMed ID12758078
JournalJ Mol Biol
Year2003
Volume329
Pages311-22
AuthorsLowry DF, Hoyt DW, Khazi FA, Bagu J, Lindsey AG, Wilson DM 3rd
TitleInvestigation of the role of the histidine-aspartate pair in the human exonuclease III-like abasic endonuclease, Ape1.

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.

createdupdated
2002-07-012009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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