EzCatDB: D00266

DB codeD00266
RLCP classification3.940.275890.113
5.300.550500.6111
6.20.8010.6100
CATH domainDomain 11.10.340.30Catalytic domain
Domain 21.10.1670.10Catalytic domain
E.C.4.2.99.18
CSA2abk

CATH domainRelated DB codes (homologues)
1.10.1670.10D00511,T00070
1.10.340.30S00749,D00511,T00070

Enzyme Name
Swiss-protKEGG

P0AB83P39788
Protein nameEndonuclease IIIProbable endonuclease IIIDNA-(apurinic or apyrimidinic site) lyase
AP lyase
AP endonuclease class I
endodeoxyribonuclease (apurinic or apyrimidinic)
deoxyribonuclease (apurinic or apyrimidinic)
E. coli endonuclease III
phage-T4 UV endonuclease
Micrococcus luteus UV endonuclease
AP site-DNA 5'-phosphomonoester-lyase
X-ray endonuclease III
SynonymsEC 4.2.99.18
DNA-(apurinic or apyrimidinic site) lyase
EC 4.2.99.18
DNA-(apurinic or apyrimidinic site) lyase


Swiss-prot:Accession NumberP0AB83P39788
Entry nameEND3_ECOLIEND3_BACSU
ActivityThe C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5''-phosphate.The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
SubunitMonomer.
Subcellular location

CofactorBinds 1 4Fe-4S cluster. The cluster is not important for the catalytic activity, but which is probably involved in the proper positioning of the enzyme along the DNA strand.Binds 1 4Fe-4S cluster. The cluster is not important for the catalytic activity, but which is probably involved in the proper positioning of the enzyme along the DNA strand (By similarity).


CofactorsSubstratesProductsintermediates
KEGG-idL00024C02270C03484C00578L00013
Compound[4Fe-4S]Base-removed DNAApyrimidinic site in DNADNA 5'-phosphateDNA 3'-trans-alpha,beta unsaturated aldehyde
Typeheavy metal,sulfide groupcarbohydrate,nucleic acids,phosphate group/phosphate ionnucleic acidsnucleic acids,phosphate group/phosphate ionnucleic acids,carbohydrate
1abkA01UnboundUnboundUnboundUnboundUnboundUnbound
2abkA01UnboundUnboundUnboundUnboundUnboundUnbound
1ornA01UnboundUnboundUnboundUnboundUnboundUnbound
1orpA01UnboundUnboundUnboundUnboundUnboundUnbound
1p59A01UnboundUnboundUnboundUnboundUnboundUnbound
1abkA02Bound:FS4UnboundUnboundUnboundUnboundUnbound
2abkA02Bound:SF4UnboundUnboundUnboundUnboundUnbound
1ornA02Bound:SF4UnboundUnboundUnboundUnboundIntermediate-bound:G-T-C-C-A-PED-G-T-C-T(chain C)
1orpA02Bound:SF4UnboundUnboundUnboundUnboundIntermediate-bound:G-T-C-C-A-PED-G-T-C-T(chain C)
1p59A02Bound:SF4UnboundAnalogue:G-5IU-C-C-A-3DR-G-5IU-C-T(chain C)UnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P0AB83 & PDB;2abk
pdbCatalytic residuesCofactor-binding residues
1abkA01ASP 44;LYS 120

2abkA01ASP 44;LYS 120

1ornA01ASP 45;LYS 121

1orpA01ASP 45;LYS 121

1p59A01ASP 45;LYS 121

1abkA02ASP 138
CYS 187;CYS 194;CYS 197;CYS 203(Iron-sulfur binding)
2abkA02ASP 138
CYS 187;CYS 194;CYS 197;CYS 203(Iron-sulfur binding)
1ornA02ASP 139
CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)
1orpA02ASP 139
CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)
1p59A02ASP 139
CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Scheme I, Scheme II, Scheme III
[7]p.439-440
[8]p.220
[12]p.4116-4117
[13]

[16]Fig.2, Fig.3, p.257-263
[20]

[27]p.3466-3468

references
[1]
PubMed ID2471512
JournalBiochem J
Year1989
Volume259
Pages751-9
AuthorsBailly V, Sente B, Verly WG
TitleBacteriophage-T4 and Micrococcus luteus UV endonucleases are not endonucleases but beta-elimination and sometimes beta delta-elimination catalysts.
[2]
PubMed ID2675965
JournalBiochemistry
Year1989
Volume28
Pages6164-70
AuthorsBoorstein RJ, Hilbert TP, Cadet J, Cunningham RP, Teebor GW
TitleUV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activities.
[3]
PubMed ID2548577
JournalBiochemistry
Year1989
Volume28
Pages4450-5
AuthorsCunningham RP, Asahara H, Bank JF, Scholes CP, Salerno JC, Surerus K, Munck E, McCracken J, Peisach J, Emptage MH
TitleEndonuclease III is an iron-sulfur protein.
[4]
PubMed ID1846560
JournalBiochemistry
Year1991
Volume30
Pages1119-26
AuthorsMazumder A, Gerlt JA, Absalon MJ, Stubbe J, Cunningham RP, Withka J, Bolton PH
TitleStereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys.
[5]
PubMed ID1644800
JournalJ Biol Chem
Year1992
Volume267
Pages16135-7
AuthorsFu W, O'Handley S, Cunningham RP, Johnson MK
TitleThe role of the iron-sulfur cluster in Escherichia coli endonuclease III. A resonance Raman study.
[6]
PubMed ID1522598
JournalJ Mol Biol
Year1992
Volume227
Pages347-51
AuthorsKuo CF, McRee DE, Cunningham RP, Tainer JA
TitleCrystallization and crystallographic characterization of the iron-sulfur-containing DNA-repair enzyme endonuclease III from Escherichia coli.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID93030750
PubMed ID1411536
JournalScience
Year1992
Volume258
Pages434-40
AuthorsKuo CF, McRee DE, Fisher CL, O'Handley SF, Cunningham RP, Tainer JA
TitleAtomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.
Related Swiss-protP0AB83
[8]
CommentsMUTAGENESIS OF LYS-120.
Medline ID94379627
PubMed ID8092678
JournalAnn N Y Acad Sci
Year1994
Volume726
Pages215-22
AuthorsCunningham RP, Ahern H, Xing D, Thayer MM, Tainer JA
TitleStructure and function of Escherichia coli endonuclease III.
Related Swiss-protP0AB83
[9]
PubMed ID7515054
JournalJ Biol Chem
Year1994
Volume269
Pages15318-24
AuthorsTchou J, Bodepudi V, Shibutani S, Antoshechkin I, Miller J, Grollman AP, Johnson F
TitleSubstrate specificity of Fpg protein. Recognition and cleavage of oxidatively damaged DNA.
[10]
PubMed ID7873533
JournalBiochemistry
Year1995
Volume34
Pages2528-36
AuthorsO'Handley S, Scholes CP, Cunningham RP
TitleEndonuclease III interactions with DNA substrates. 1. Binding and footprinting studies with oligonucleotides containing a reduced apyrimidinic site.
[11]
PubMed ID7873534
JournalBiochemistry
Year1995
Volume34
Pages2537-44
AuthorsXing D, Dorr R, Cunningham RP, Scholes CP
TitleEndonuclease III interactions with DNA substrates. 2. The DNA repair enzyme endonuclease III binds differently to intact DNA and to apyrimidinic/apurinic DNA substrates as shown by tryptophan fluorescence quenching.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID95393988
PubMed ID7664751
JournalEMBO J
Year1995
Volume14
Pages4108-20
AuthorsThayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA
TitleNovel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
Related PDB1abk,2abk
Related Swiss-protP0AB83
[13]
PubMed ID8960131
JournalMutat Res
Year1996
Volume364
Pages193-207
AuthorsPurmal AA, Rabow LE, Lampman GW, Cunningham RP, Kow YW
TitleA common mechanism of action for the N-glycosylase activity of DNA N-glycosylase/AP lyases from E. coli and T4.
[14]
PubMed ID9705289
JournalJ Biol Chem
Year1998
Volume273
Pages21585-93
AuthorsIkeda S, Biswas T, Roy R, Izumi T, Boldogh I, Kurosky A, Sarker AH, Seki S, Mitra S
TitlePurification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residue.
[15]
PubMed ID9808040
JournalNat Struct Biol
Year1998
Volume5
Pages959-64
AuthorsYuan YC, Whitson RH, Liu Q, Itakura K, Chen Y
TitleA novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
[16]
PubMed ID10872450
JournalAnnu Rev Biochem
Year1999
Volume68
Pages255-85
AuthorsMcCullough AK, Dodson ML, Lloyd RS
TitleInitiation of base excision repair: glycosylase mechanisms and structures.
[17]
PubMed ID10066771
JournalJ Biol Chem
Year1999
Volume274
Pages7128-36
AuthorsStierum RH, Croteau DL, Bohr VA
TitlePurification and characterization of a mitochondrial thymine glycol endonuclease from rat liver.
[18]
PubMed ID10390347
JournalJ Mol Biol
Year1999
Volume290
Pages495-504
AuthorsAihara H, Ito Y, Kurumizaka H, Yokoyama S, Shibata T
TitleThe N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
[19]
PubMed ID10467137
JournalStructure Fold Des
Year1999
Volume7
Pages919-30
AuthorsShekhtman A, McNaughton L, Cunningham RP, Baxter SM
TitleIdentification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods.
[20]
PubMed ID10675345
JournalEMBO J
Year2000
Volume19
Pages758-66
AuthorsHollis T, Ichikawa Y, Ellenberger T
TitleDNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
[21]
PubMed ID11341839
JournalBiochemistry
Year2001
Volume40
Pages5738-46
AuthorsDavid-Cordonnier MH, Laval J, O'Neill P
TitleRecognition and kinetics for excision of a base lesion within clustered DNA damage by the Escherichia coli proteins Fpg and Nth.
[22]
PubMed ID11259435
JournalJ Biol Chem
Year2001
Volume276
Pages21821-7
AuthorsSpeina E, Ciesla JM, Wojcik J, Bajek M, Kusmierek JT, Tudek B
TitleThe pyrimidine ring-opened derivative of 1,N6-ethenoadenine is excised from DNA by the Escherichia coli Fpg and Nth proteins.
[23]
PubMed ID11960995
JournalJ Biol Chem
Year2002
Volume277
Pages22605-15
AuthorsPope MA, Porello SL, David SS
TitleEscherichia coli apurinic-apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G:A substrates.
[24]
PubMed ID12144783
JournalJ Mol Biol
Year2002
Volume321
Pages265-76
AuthorsLiu X, Roy R
TitleTruncation of amino-terminal tail stimulates activity of human endonuclease III (hNTH1).
[25]
PubMed ID11786018
JournalJ Mol Biol
Year2002
Volume315
Pages373-84
AuthorsMol CD, Arvai AS, Begley TJ, Cunningham RP, Tainer JA
TitleStructure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.
[26]
PubMed ID11911468
JournalMol Cells
Year2002
Volume13
Pages154-6
AuthorsLee CH, Kim SH, Choi JI, Choi JY, Lee CE, Kim J
TitleElectron paramagnetic resonance study reveals a putative iron-sulfur cluster in human rpS3 protein.
[27]
PubMed ID12840008
JournalEMBO J
Year2003
Volume22
Pages3461-71
AuthorsFromme JC, Verdine GL
TitleStructure of a trapped endonuclease III-DNA covalent intermediate.
Related PDB1orn,1orp,1p59

comments
E.C. 3.1.25.2 was transferred to E.C. 4.2.99.18.
Although this enzyme has got an iron-sulfur cluster, it serves to stabilize the protein fold rather than acts as a cofactor (see [27]).
Endonuclease iii acts as not only a AP lyase (catalysis at LYS 120) but also a N-glycosylase (catalysis at GLU 112) (see [7]).
According to the literature [16] & [27], this enzyme catalyzes several reactions. Formation of Schiff-base with Lys121 involves (A) Sugar ring opening (or glycosyl transfer to Lys121) and (B) C1' dehydration (or eliminative double-bond formation). In contrast, lyase reaction after the Schiff-base formation involves (C) elimination of 3'-phosphate group (or Eliminative double-bond formation) and (D) Deformation of Schiff-base from Lys121 (Exchange of double-bonded bond).
The reactions proceed as follows (see [16], [20] & [27]):
(A) Sugar ring opening (glycosyl transfer to Lys121)
(A1) The reaction proceeds via SN1-like mechanism.
(A2) A general acid protonates the leaving O4' atom of the DNA deoxyribose, forming an oxocarbonium ion. Asp45 may act as the acid, considering the PDB structure (1p59), and then stabilize the intermediate.
(A3) The acceptor, Lys121, is activated by a general base, Asp139.
(A4) The activated acceptor, Lys121, makes a nucleophilic attack on the transferred group, C1' atom of the deoxyribose, forming a covalent bond with it. This reaction generates a tetrahedral intermediate at C1' atom, releasing the O4' atom.
(B) C1' dehydration (or eliminative double-bond formation)
Although the mechanism of this reaction is not clear, at least the lone pair of Lys121 makes a nucleophilic attack on C1' atom, whilst a general acid (conserved Ser40?) protonates the eliminated hydroxyl group (1'-OH).
(C) elimination of 3'-phosphate group (or Eliminative double-bond formation) (see [8], [16], [27])
(C1) The reaction may proceed via E2 mechanism (see [8]).
(C2) The protonated Schiff-base acts as an "electron sink" (or modulator), by lowering the pKa of 2'-hydrogen. (see [16]).
(C3) Asp45 acts as a general base to abstract C2'-pro-R hydrogen, through a water molecule. (see [27])
(C4) At the same time, Asp139 acts as a general acid to protonate the eliminated 3'-phosphate oxygen.
(D) Deformation of Schiff-base from Lys121 (Exchange of double-bonded bond).
Although the mechanism of this reaction is not clear, a water, which must be activated bya base (Asp139) makes a nucleophilic attack on C1' atom, forming a tetrahedral intermediate. And then, the lone pair of the new hydroxyl group makes a nucleophilic attack on C1' atom, whilst a general acid (Asp139 ?) protonates the leaving Lys121.

createdupdated
2004-07-212009-09-29


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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