Escherichia coli K-12 substr. MG1655 Enzyme: endonuclease III; specific for apurinic and/or apyrimidinic sites

Gene: nth Accession Numbers: EG10662 (EcoCyc), b1633, ECK1629

Synonyms: Endo III

Regulation Summary Diagram: ?

Regulation summary diagram for nth

Endonuclease III (Nth) is a DNA glycosylase that recognizes pyrimidine residues damaged by ring saturation, ring fragmentation or ring contraction. Examples of these types of damage include thymine glycol, 5,6-dihydrouracil, 5-hydroxy-6-hydrouracil, 5-2'-deoxyctidine and 5-hydroxy-2'-deoxyuridine [Purmal98, Breimer84, Hatahet94]. Nth has been shown to act in the process of base excision repair (BER). BER works to repair damaged DNA by multiple steps: removal of the AP site by an AP endonuclease; resynthesis of the excised strand by DNA ligase. Although Nth has been shown to display an AP lyase activity [Kim88], complete processing of Nth substrates is believed to require the further action of an additional AP endonuclease followed by DNA polymerase and DNA ligase. Nth has been overexpressed and purified [Asahara89] and its crystal structure has been solved to 2 Å [Kuo92]. Endonuclease III is observed to crosslink to 2-deoxyribonolactone DNA lesions; such lesions interfere with endonuclease III excision repair of abasic lesions [Kroeger03].

Gene Citations: [Gifford00]

Locations: cytosol

Map Position: [1,709,547 -> 1,710,182] (36.85 centisomes, 133°)
Length: 636 bp / 211 aa

Molecular Weight of Polypeptide: 23.562 kD (from nucleotide sequence), 27.3 kD (experimental) [Asahara89 ]

Unification Links: ASAP:ABE-0005463 , CGSC:13070 , DIP:DIP-48071N , EchoBASE:EB0656 , EcoGene:EG10662 , EcoliWiki:b1633 , Mint:MINT-1223379 , ModBase:P0AB83 , OU-Microarray:b1633 , PortEco:nth , PR:PRO_000023419 , Protein Model Portal:P0AB83 , RefSeq:NP_416150 , RegulonDB:EG10662 , SMR:P0AB83 , String:511145.b1633 , UniProt:P0AB83

Relationship Links: InterPro:IN-FAMILY:IPR000445 , InterPro:IN-FAMILY:IPR003265 , InterPro:IN-FAMILY:IPR003583 , InterPro:IN-FAMILY:IPR003651 , InterPro:IN-FAMILY:IPR004035 , InterPro:IN-FAMILY:IPR004036 , InterPro:IN-FAMILY:IPR005759 , InterPro:IN-FAMILY:IPR011257 , InterPro:IN-FAMILY:IPR023170 , PDB:Structure:2ABK , Pfam:IN-FAMILY:PF00633 , Pfam:IN-FAMILY:PF00730 , Pfam:IN-FAMILY:PF10576 , Prosite:IN-FAMILY:PS00764 , Prosite:IN-FAMILY:PS01155 , Smart:IN-FAMILY:SM00278 , Smart:IN-FAMILY:SM00478 , Smart:IN-FAMILY:SM00525

In Paralogous Gene Group: 322 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0000737 - DNA catabolic process, endonucleolytic Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0006284 - base-excision repair Inferred by computational analysis [GOA01a]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003906 - DNA-(apurinic or apyrimidinic site) lyase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Asahara89]
GO:0005515 - protein binding Inferred from experiment [Butland05]
GO:0019104 - DNA N-glycosylase activity Inferred from experiment Inferred by computational analysis [GOA06, Asahara89]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016798 - hydrolase activity, acting on glycosyl bonds Inferred by computational analysis [UniProtGOA11a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection radiation
information transfer DNA related DNA degradation
metabolism degradation of macromolecules DNA

Essentiality data for nth knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Enzymatic reaction of: DNA-AP site lyase (endonuclease III; specific for apurinic and/or apyrimidinic sites)

EC Number:

a DNA containing an apurinic/apyrimidinic site <=> a 5'-phosphopolynucleotide + a 3'-terminal unsaturated sugar

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Enzymatic reaction of: DNA glycosylase (endonuclease III; specific for apurinic and/or apyrimidinic sites)

EC Number:

a damaged DNA pyrimidine <=> a DNA containing an apyrimidinic site

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Sequence Features

Protein sequence of endonuclease III; specific for apurinic and/or apyrimidinic sites with features indicated

Feature Class Location Citations Comment
Conserved-Region 108 -> 127
UniProt: HhH.
Mutagenesis-Variant 120
[Thayer95, UniProt13]
UniProt: 100000-fold decrease in activity and slight decrease in substrate affinity.
Mutagenesis-Variant 138
[Thayer95, UniProt13]
UniProt: 100-fold decrease in activity and 4-fold increase in substrate affinity.
Metal-Binding-Site 187
UniProt: Iron-sulfur (4Fe-4S).
Mutagenesis-Variant 191
[Thayer95, UniProt13]
UniProt: Slight decrease in activity and 130-fold increase in substrate affinity.
Metal-Binding-Site 194
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 197
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 203
UniProt: Iron-sulfur (4Fe-4S).

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1633 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10662; confirmed by SwissProt match.


Asahara89: Asahara H, Wistort PM, Bank JF, Bakerian RH, Cunningham RP (1989). "Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene." Biochemistry 28(10);4444-9. PMID: 2669955

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Breimer84: Breimer LH, Lindahl T (1984). "DNA glycosylase activities for thymine residues damaged by ring saturation, fragmentation, or ring contraction are functions of endonuclease III in Escherichia coli." J Biol Chem 259(9);5543-8. PMID: 6371006

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gifford00: Gifford CM, Wallace SS (2000). "The genes encoding endonuclease VIII and endonuclease III in Escherichia coli are transcribed as the terminal genes in operons." Nucleic Acids Res 28(3);762-9. PMID: 10637328

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hatahet94: Hatahet Z, Kow YW, Purmal AA, Cunningham RP, Wallace SS (1994). "New substrates for old enzymes. 5-Hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase, while 5-hydroxy-2'-deoxyuridine is a substrate for uracil DNA N-glycosylase." J Biol Chem 269(29);18814-20. PMID: 8034633

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kim88: Kim J, Linn S (1988). "The mechanisms of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites." Nucleic Acids Res 16(3);1135-41. PMID: 2449657

Kroeger03: Kroeger KM, Hashimoto M, Kow YW, Greenberg MM (2003). "Cross-linking of 2-deoxyribonolactone and its beta-elimination product by base excision repair enzymes." Biochemistry 42(8);2449-55. PMID: 12600212

Kuo92: Kuo CF, McRee DE, Fisher CL, O'Handley SF, Cunningham RP, Tainer JA (1992). "Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III." Science 258(5081);434-40. PMID: 1411536

Purmal98: Purmal AA, Lampman GW, Bond JP, Hatahet Z, Wallace SS (1998). "Enzymatic processing of uracil glycol, a major oxidative product of DNA cytosine." J Biol Chem 273(16);10026-35. PMID: 9545349

Thayer95: Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA (1995). "Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure." EMBO J 14(16);4108-20. PMID: 7664751

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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