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MetaCyc Enzyme: DNA-specific endonuclease I

Gene: endA Accession Numbers: EG11336 (MetaCyc), b2945, ECK2940

Species: Escherichia coli K-12 substr. MG1655

Summary:
Endonuclease I is a periplasmic enzyme that cleaves within duplex DNA. Its cellular role is unknown.

Endonuclease I cleaves within duplex DNA, producing oligonucleotides that are on average 7 bp long and contain 5' phosphate groups [Lehman62]. It is inhibited by tRNA and rRNA [Lehman62a].

Mutants lacking endA show no apparent difference from wild type cells [Durwald68, Wright71]. A UV-resistant mutant had increased DNA polymerase I and endonuclease I activity [Ahmad80].

EndA: endonuclease I [Wright71]

Citations: [Bernardi65, Richardson66, Molholt68, Eigner68, Goebel70, Bernardi75, McIntosh75, Ananthaswamy76, Ananthaswamy77, Khachatourians79, Lin92b, Taylor93a, Jekel94, Wnendt94, Cherepanov95, Akaboshi99, Griffith03, Akaboshi05, Yau08, Borja12]

Locations: periplasmic space

Map Position: [3,088,369 -> 3,089,076]

Molecular Weight of Polypeptide: 26.709 kD (from nucleotide sequence), 25.0 kD (experimental) [Jekel95 ]

Unification Links: ASAP:ABE-0009661 , CGSC:824 , EchoBASE:EB1312 , EcoGene:EG11336 , EcoliWiki:b2945 , ModBase:P25736 , OU-Microarray:b2945 , PortEco:endA , PR:PRO_000022515 , Protein Model Portal:P25736 , RefSeq:NP_417420 , RegulonDB:EG11336 , SMR:P25736 , String:511145.b2945 , Swiss-Model:P25736 , UniProt:P25736

Relationship Links: InterPro:IN-FAMILY:IPR007346 , Pfam:IN-FAMILY:PF04231

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006308 - DNA catabolic process Inferred from experiment [Wright71]
Molecular Function: GO:0004519 - endonuclease activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Goebel70]
GO:0016888 - endodeoxyribonuclease activity, producing 5'-phosphomonoesters Inferred from experiment [Lehman62]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004530 - deoxyribonuclease I activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09, Cordonnier65]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: information transfer DNA related DNA degradation
metabolism degradation of macromolecules DNA

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


Enzymatic reaction of: endonuclease I

EC Number: 3.1.21.1

a double stranded DNA[periplasmic space] + n H2O[periplasmic space] <=> n+1 a 5'-phosphooligonucleotide[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Summary:
The enzyme was initially purified from E. coli B [Lehman62, Lehman62a, Melgar68, Ehrlich73a].

Citations: [Jekel95]

Cofactors or Prosthetic Groups: Mg2+ [Goebel70]

Inhibitors (Unknown Mechanism): a tRNA [Goebel70]

pH(opt): 7.5-8.5 [Lehman62]


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 22
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Chain 23 -> 235
[UniProt09]
UniProt: Endonuclease-1;

History:
10/20/97 Gene b2945 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11336; confirmed by SwissProt match.


References

Ahmad80: Ahmad SI, Atkinson A, Eisenstark A (1980). "Isolation and characterization of a mutant of Escherichia coli K12 synthesizing DNA polymerase I and endonuclease I constitutively." J Gen Microbiol 117(2);419-22. PMID: 6252282

Akaboshi05: Akaboshi E (2005). "Dynamic profiles of DNA: analysis of CAP- and LexA protein-binding regions with endonucleases." DNA Cell Biol 24(3);161-72. PMID: 15767782

Akaboshi99: Akaboshi E (1999). "Recognition of sequence-directed structure of the ssDNA backbone by nucleases." Biochem Biophys Res Commun 256(3);532-6. PMID: 10080932

Ananthaswamy76: Ananthaswamy HN (1976). "The release of endonuclease I from Escherichia coli by a new cold shock procedure." Biochem Biophys Res Commun 76(2);289-98. PMID: 194597

Ananthaswamy77: Ananthaswamy HN (1977). "Release of periplasmic enzymes from Escherichia coli by penicillin-ethylenediaminetetraacetate treatment." J Bacteriol 131(2);710-2. PMID: 195932

Bernardi65: Bernardi G, Cordonnier C (1965). "Mechanism of degradation of DNA by endonuclease I from Escherichia coli." J Mol Biol 11;141-3. PMID: 14255756

Bernardi75: Bernardi A, Gaillard C, Bernardi G (1975). "The specificity of five DNAases as studied by the analysis of 5'-terminal doublets." Eur J Biochem 52(3);451-7. PMID: 800985

Borja12: Borja GM, Meza Mora E, Barron B, Gosset G, Ramirez OT, Lara AR (2012). "Engineering Escherichia coli to increase plasmid DNA production in high cell-density cultivations in batch mode." Microb Cell Fact 11;132. PMID: 22992433

Cherepanov95: Cherepanov PP, Wackernagel W (1995). "Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant." Gene 158(1);9-14. PMID: 7789817

Cordonnier65: Cordonnier C, Bernardi G (1965). "Localization of E. coli endonuclease I." Biochem Biophys Res Commun 20(5);555-9. PMID: 4955462

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

Durwald68: Durwald H, Hoffmann-Berling H (1968). "Endonuclease-I-deficient and ribonuclease I-deficient Escherichia coli mutants." J Mol Biol 34(2);331-46. PMID: 4938550

Eberhard72: Eberhard C, Herrmann RL (1972). "Effect of deoxyribonucleic acid ligands on deoxyribonucleases and deoxyribonucleic acid polymerase I of Escherichia coli K-12." J Bacteriol 112(1);224-30. PMID: 4562396

Ehrlich73a: Ehrlich SD, Bertazzoni U, Bernardi G (1973). "The specificity of Escherichia coli endonuclease I." Eur J Biochem 40(1);149-53. PMID: 4589547

Eigner68: Eigner J, Block S (1968). "Host-controlled restriction of T-even bacteriophages: relation of four bacterial deoxyribonucleases to restriction." J Virol 2(4);320-6. PMID: 4911846

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."

Goebel70: Goebel W, Helinski DR (1970). "Nicking activity of an endonuclease. I. Transfer ribonucleic acid complex of Escherichia coli." Biochemistry 9(24);4793-801. PMID: 4991605

Griffith03: Griffith M, Gietz RD (2003). "Escherichia coli endA deletion strain for use in two-hybrid shuttle vector selection." Biotechniques 35(2);272-4, 276, 278. PMID: 12951767

Jekel94: Jekel M, Wackernagel W (1994). "Location of the endA gene coding for endonuclease I on the physical map of the Escherichia coli K-12 chromosome." J Bacteriol 176(5);1550-1. PMID: 8113204

Jekel95: Jekel M, Wackernagel W (1995). "The periplasmic endonuclease I of Escherichia coli has amino-acid sequence homology to the extracellular DNases of Vibrio cholerae and Aeromonas hydrophila." Gene 154(1);55-9. PMID: 7867949

Khachatourians79: Khachatourians GG (1979). "Escherichia coli Hfr-DNA degradation in endonuclease I-deficient minicells." Biochim Biophys Acta 561(2);294-300. PMID: 371681

Lehman62: Lehman IR, Roussos GG, Pratt EA (1962). "The deoxyribonucleases of Escherichia coli. II. Purification and properties of a ribonucleic acid-inhibitable endonuclease." J Biol Chem 237;819-28. PMID: 14463751

Lehman62a: Lehman IR, Roussos GG, Pratt EA (1962). "The deoxyribo-nucleases of Escherichia coli. III. Studies on the nature of the inhibition of endonuclease by ribonucleic acid." J Biol Chem 237;829-33. PMID: 14463750

Lin92b: Lin JJ (1992). "Endonuclease A degrades chromosomal and plasmid DNA of Escherichia coli present in most preparations of single stranded DNA from phagemids." Proc Natl Sci Counc Repub China B 16(1);1-5. PMID: 1631242

McIntosh75: McIntosh MA, Earhart CF (1975). "Effect of ribonuclease on the association of deoxyribonucleic acid with the membrane in Escherichia coli." J Bacteriol 122(2);592-8. PMID: 1092660

Melgar68: Melgar E, Goldthwait DA (1968). "Deoxyribonucleic acid nucleases. I. The use of a new method to observe the kinetics of deoxyribonucleic acid degradation by deoxyribonuclease I, deoxyribonuclease II, and Escherichia coli endonuclease I." J Biol Chem 243(17);4401-8. PMID: 4879164

Molholt68: Molholt B, Fraser D (1968). "Host-controlled restriction of T-even bacteriophages: relation of endonuclease I and T-even-induced nucleases to restriction." J Virol 2(4);313-9. PMID: 4911845

Richardson66: Richardson CC (1966). "Influence of glucosylation of deoxyribonucleic acid on hydrolysis by deoxyribonucleases of Escherichia coli." J Biol Chem 241(9);2084-92. PMID: 4287760

Taylor93a: Taylor RG, Walker DC, McInnes RR (1993). "E. coli host strains significantly affect the quality of small scale plasmid DNA preparations used for sequencing." Nucleic Acids Res 21(7);1677-8. PMID: 8479929

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Wnendt94: Wnendt S (1994). "Analysis of the endA mutation of Escherichia coli K12 strains: JM103 behaves like endA+ wild-type strains." Biotechniques 17(2);270, 272. PMID: 7980923

Wright71: Wright M (1971). "Mutants of Escherichia coli lacking endonuclease I, ribonuclease I, or ribonuclease II." J Bacteriol 107(1);87-94. PMID: 4105037

Yau08: Yau SY, Keshavarz-Moore E, Ward J (2008). "Host strain influences on supercoiled plasmid DNA production in Escherichia coli: Implications for efficient design of large-scale processes." Biotechnol Bioeng 101(3);529-44. PMID: 18438778


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Wed Sep 2, 2015, biocyc13.