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
CATH 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 33725
PubChem

1abkA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2abkA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1ornA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1orpA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1p59A01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1abkA02	Bound:FS4	Unbound	Unbound	Unbound	Unbound	Unbound
2abkA02	Bound:SF4	Unbound	Unbound	Unbound	Unbound	Unbound
1ornA02	Bound:SF4	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:G-T-C-C-A-PED-G-T-C-T (chain C)
1orpA02	Bound:SF4	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:G-T-C-C-A-PED-G-T-C-T (chain C)
1p59A02	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	ASP 44;LYS 120
2abkA01	ASP 44;LYS 120
1ornA01	ASP 45;LYS 121
1orpA01	ASP 45;LYS 121
1p59A01	ASP 45;LYS 121
1abkA02	ASP 138	CYS 187;CYS 194;CYS 197;CYS 203(Iron-sulfur binding)
2abkA02	ASP 138	CYS 187;CYS 194;CYS 197;CYS 203(Iron-sulfur binding)
1ornA02	ASP 139	CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)
1orpA02	ASP 139	CYS 189;CYS 196;CYS 199;CYS 205(Iron-sulfur binding)
1p59A02	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.

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