DB code: D00266

RLCP classification 3.940.275890.113 : Transfer
5.300.550500.6111 : Elimination
6.20.8010.6100 : Double-bonded atom exchange
CATH domain 1.10.340.30 : Endonuclease III; domain 1 Catalytic domain
1.10.1670.10 : Endonuclease Iii, domain 2 Catalytic domain
E.C. 4.2.99.18
CSA 2abk
M-CSA 2abk
MACiE

CATH domain Related DB codes (homologues)
1.10.1670.10 : Endonuclease Iii, domain 2 D00511 T00070
1.10.340.30 : Endonuclease III; domain 1 S00749 D00511 T00070

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AB83 Endonuclease III
EC 4.2.99.18
DNA-(apurinic or apyrimidinic site) lyase
NP_416150.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489897.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF10576 (EndIII_4Fe-2S)
PF00633 (HHH)
PF00730 (HhH-GPD)
[Graphical View]
P39788 Endonuclease III
EC 4.2.99.18
DNA-(apurinic or apyrimidinic site) lyase
NP_390115.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF00633 (HHH)
PF00730 (HhH-GPD)
[Graphical View]

KEGG enzyme name
DNA-(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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0AB83 END3_ECOLI 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. Monomer. 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.
P39788 END3_BACSU 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. 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).

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id L00024 C02270 C03484 C00578 L00013
E.C.
Compound [4Fe-4S] Base-removed DNA Apyrimidinic site in DNA DNA 5'-phosphate DNA 3'-trans-alpha,beta unsaturated aldehyde
Type heavy metal,sulfide group carbohydrate,nucleic acids,phosphate group/phosphate ion nucleic acids nucleic acids,phosphate group/phosphate ion nucleic acids,carbohydrate
ChEBI 33725
PubChem
1abkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
2abkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ornA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1orpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1p59A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1abkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FS4 Unbound Unbound Unbound Unbound Unbound
2abkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SF4 Unbound Unbound Unbound Unbound Unbound
1ornA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SF4 Unbound Unbound Unbound Unbound Intermediate-bound:G-T-C-C-A-PED-G-T-C-T (chain C)
1orpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SF4 Unbound Unbound Unbound Unbound Intermediate-bound:G-T-C-C-A-PED-G-T-C-T (chain C)
1p59A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SF4 Unbound Analogue:G-5IU-C-C-A-3DR-G-5IU-C-T (chain C) Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0AB83 & PDB;2abk

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1abkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 44;LYS 120
2abkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 44;LYS 120
1ornA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 45;LYS 121
1orpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 45;LYS 121
1p59A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 45;LYS 121
1abkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 138 CYS 187;CYS 194;CYS 197;CYS 203(Iron-sulfur binding)
2abkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 138 CYS 187;CYS 194;CYS 197;CYS 203(Iron-sulfur binding)
1ornA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 139 CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)
1orpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 139 CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)
1p59A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 139 CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 2471512
Journal Biochem J
Year 1989
Volume 259
Pages 751-9
Authors Bailly V, Sente B, Verly WG
Title Bacteriophage-T4 and Micrococcus luteus UV endonucleases are not endonucleases but beta-elimination and sometimes beta delta-elimination catalysts.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2675965
Journal Biochemistry
Year 1989
Volume 28
Pages 6164-70
Authors Boorstein RJ, Hilbert TP, Cadet J, Cunningham RP, Teebor GW
Title UV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activities.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2548577
Journal Biochemistry
Year 1989
Volume 28
Pages 4450-5
Authors Cunningham RP, Asahara H, Bank JF, Scholes CP, Salerno JC, Surerus K, Munck E, McCracken J, Peisach J, Emptage MH
Title Endonuclease III is an iron-sulfur protein.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1846560
Journal Biochemistry
Year 1991
Volume 30
Pages 1119-26
Authors Mazumder A, Gerlt JA, Absalon MJ, Stubbe J, Cunningham RP, Withka J, Bolton PH
Title Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 1644800
Journal J Biol Chem
Year 1992
Volume 267
Pages 16135-7
Authors Fu W, O'Handley S, Cunningham RP, Johnson MK
Title The role of the iron-sulfur cluster in Escherichia coli endonuclease III. A resonance Raman study.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 1522598
Journal J Mol Biol
Year 1992
Volume 227
Pages 347-51
Authors Kuo CF, McRee DE, Cunningham RP, Tainer JA
Title Crystallization and crystallographic characterization of the iron-sulfur-containing DNA-repair enzyme endonuclease III from Escherichia coli.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 93030750
PubMed ID 1411536
Journal Science
Year 1992
Volume 258
Pages 434-40
Authors Kuo CF, McRee DE, Fisher CL, O'Handley SF, Cunningham RP, Tainer JA
Title Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.
Related PDB
Related UniProtKB P0AB83
[8]
Resource
Comments MUTAGENESIS OF LYS-120.
Medline ID 94379627
PubMed ID 8092678
Journal Ann N Y Acad Sci
Year 1994
Volume 726
Pages 215-22
Authors Cunningham RP, Ahern H, Xing D, Thayer MM, Tainer JA
Title Structure and function of Escherichia coli endonuclease III.
Related PDB
Related UniProtKB P0AB83
[9]
Resource
Comments
Medline ID
PubMed ID 7515054
Journal J Biol Chem
Year 1994
Volume 269
Pages 15318-24
Authors Tchou J, Bodepudi V, Shibutani S, Antoshechkin I, Miller J, Grollman AP, Johnson F
Title Substrate specificity of Fpg protein. Recognition and cleavage of oxidatively damaged DNA.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 7873533
Journal Biochemistry
Year 1995
Volume 34
Pages 2528-36
Authors O'Handley S, Scholes CP, Cunningham RP
Title Endonuclease III interactions with DNA substrates. 1. Binding and footprinting studies with oligonucleotides containing a reduced apyrimidinic site.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 7873534
Journal Biochemistry
Year 1995
Volume 34
Pages 2537-44
Authors Xing D, Dorr R, Cunningham RP, Scholes CP
Title Endonuclease 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.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID 95393988
PubMed ID 7664751
Journal EMBO J
Year 1995
Volume 14
Pages 4108-20
Authors Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA
Title Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
Related PDB 1abk 2abk
Related UniProtKB P0AB83
[13]
Resource
Comments
Medline ID
PubMed ID 8960131
Journal Mutat Res
Year 1996
Volume 364
Pages 193-207
Authors Purmal AA, Rabow LE, Lampman GW, Cunningham RP, Kow YW
Title A common mechanism of action for the N-glycosylase activity of DNA N-glycosylase/AP lyases from E. coli and T4.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9705289
Journal J Biol Chem
Year 1998
Volume 273
Pages 21585-93
Authors Ikeda S, Biswas T, Roy R, Izumi T, Boldogh I, Kurosky A, Sarker AH, Seki S, Mitra S
Title Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residue.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 9808040
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 959-64
Authors Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y
Title A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10872450
Journal Annu Rev Biochem
Year 1999
Volume 68
Pages 255-85
Authors McCullough AK, Dodson ML, Lloyd RS
Title Initiation of base excision repair: glycosylase mechanisms and structures.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10066771
Journal J Biol Chem
Year 1999
Volume 274
Pages 7128-36
Authors Stierum RH, Croteau DL, Bohr VA
Title Purification and characterization of a mitochondrial thymine glycol endonuclease from rat liver.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 10390347
Journal J Mol Biol
Year 1999
Volume 290
Pages 495-504
Authors Aihara H, Ito Y, Kurumizaka H, Yokoyama S, Shibata T
Title The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 10467137
Journal Structure Fold Des
Year 1999
Volume 7
Pages 919-30
Authors Shekhtman A, McNaughton L, Cunningham RP, Baxter SM
Title Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 10675345
Journal EMBO J
Year 2000
Volume 19
Pages 758-66
Authors Hollis T, Ichikawa Y, Ellenberger T
Title DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11341839
Journal Biochemistry
Year 2001
Volume 40
Pages 5738-46
Authors David-Cordonnier MH, Laval J, O'Neill P
Title Recognition and kinetics for excision of a base lesion within clustered DNA damage by the Escherichia coli proteins Fpg and Nth.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11259435
Journal J Biol Chem
Year 2001
Volume 276
Pages 21821-7
Authors Speina E, Ciesla JM, Wojcik J, Bajek M, Kusmierek JT, Tudek B
Title The pyrimidine ring-opened derivative of 1,N6-ethenoadenine is excised from DNA by the Escherichia coli Fpg and Nth proteins.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 11960995
Journal J Biol Chem
Year 2002
Volume 277
Pages 22605-15
Authors Pope MA, Porello SL, David SS
Title Escherichia coli apurinic-apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G:A substrates.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12144783
Journal J Mol Biol
Year 2002
Volume 321
Pages 265-76
Authors Liu X, Roy R
Title Truncation of amino-terminal tail stimulates activity of human endonuclease III (hNTH1).
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 11786018
Journal J Mol Biol
Year 2002
Volume 315
Pages 373-84
Authors Mol CD, Arvai AS, Begley TJ, Cunningham RP, Tainer JA
Title Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11911468
Journal Mol Cells
Year 2002
Volume 13
Pages 154-6
Authors Lee CH, Kim SH, Choi JI, Choi JY, Lee CE, Kim J
Title Electron paramagnetic resonance study reveals a putative iron-sulfur cluster in human rpS3 protein.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 12840008
Journal EMBO J
Year 2003
Volume 22
Pages 3461-71
Authors Fromme JC, Verdine GL
Title Structure of a trapped endonuclease III-DNA covalent intermediate.
Related PDB 1orn 1orp 1p59
Related UniProtKB

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.

Created Updated
2004-07-21 2009-09-29