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Exodeoxyribonuclease I
Identifiers
EC no.3.1.11.1
CAS no.9037-46-1
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
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PMCarticles
PubMedarticles
NCBIproteins

Exodeoxyribonuclease I (EC 3.1.11.1, Escherichia coli exonuclease I, E. coli exonuclease I, exonuclease I) is an enzyme[1][2][3] that catalyses the following chemical reaction:

Exonucleolytic cleavage in the 3′- to 5′-direction to yield nucleoside 5′-phosphates and has been implicated in DNA recombination and repair[4].

Preference for[clarification needed] single-stranded DNA. The Escherichia coli enzyme hydrolyses glucosylated DNA.

EC number of the enzyme

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The EC number of Exodeoxyribonuclease I is 3.1.11.1. The first number 3 means that it is in class 3 which is hydrolases enzymes. EC 3.1 are the esterases. EC 3.1.11-31 are nucleases including deoxyribonuclease (DNase) and ribonuclease (RNase). EC 3.1.11-16 are exonucleases and EC 3.1.21-31 are endonucleases. EC 3.1.11 is exodeoxyribonucleases producing 5’-phosphomonoesters[5][6]. The serial number is 1.

Reaction pathway

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Exodeoxyribonuclease I conduct exonucleolytic cleavage in the direction of 3' to 5' and yield nucleoside 5'-phosphates. It hydrolyzes single stranded DNA via a metal catalytic mechanism which requires two divalent metal ions, Mg2+[4][7][8][9]. Two metal ions are in the active site, establishing a pattern for phosphodiester bond hydrolysis. One of the divalent ion is presumed to initiate the hydrolysis of phosphodiester bond between DNA by forming the attacking hydroxide ion; the other stabilizes the pentacoordinated transition state and/or oxyanion leaving-group[10].

Organism

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Exonuclease I (ExoI) is found in Escherichia coli[7][8]. ExoI seems to be discovered only in gamma-proteobacteria and not widespread[10].

Enzyme function (in cell)

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Exonuclease I is reported to be involved in the process of DNA genetic recombination, mutation avoidance, and repair in E. coli[4]. In bacteria, the lesions of single-stranded DNA and double-stranded DNA might happen due to the contact between the chromosome and cytoplasm, radicals, and other chemicals[11]. Therefore, they evolve the DNA repair mechanisms to resist these reactions. In the beginning, Exonuclease I (ExoI) was recognized as the suppressor of recombination in recBC mutants, yet the subsequent research states that the multiple exonuclease in E. coli play important roles in the recombination and repair pathways[12][13]. The specific requirement of ExoI in apurinic or apyrimidinic sites repair suggests the possible effect on the correct alignment and suppression of mutations[14][15][16]. Methyl-directed mismatch repair/correction (MMR) in E. coli requires the following protein components: MutHLS reaction (MutS, MutL, MutH) for activation of MutH endonuclease[17], four most potent exonucleases (ExoI, ExoVII, ExoX, and RecJ)[10], single-stranded DNA binding protein (SSB), DNA helicase II (MutU/UvrD), DNA polymerase III holoenzyme, and DNA ligase[18][19]. The first step of DNA repair is MutS binding to the mismatch DNA (mostly ssDNA)[20][21]. Following that, MutL will bind to heteroduplex DNA which is dependent on MutS and ATP in order to stabilize the interaction and other proteins in the repair process[22]. This complex can activate the endonuclease activity of MutH, cleaving the unmethylated strand of a hemimethylated sequence that can be on either side of the mispair DNA[22]. Initial biochemical analysis suggests the involvement of the hydrolysis of exonuclease I in 3' to 5' orientation in mismatch repair process after the strand break occurs at 3’ to the mispair DNA caused by MutH[7][18][23][24].

Crystal structure of Exodeoxyribonuclease I

Crystal structure

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The crystal structure of ExoI without DNA is reported to have a C-shaped molecule of three domains. First is an N-terminal nuclease domain (residues 1–201) that has the same relative structure to the proofreading domain of E. coli DNA polymerase I, this domain also shows the similarity of structure to other DnaQ superfamily enzymes. Second part is the central domain that the part of portion shares similarity to the SH3 domain fold (residues 202–354). Last is the C-terminal α-helical domain (residues 359–475)[25].

Active sites

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The active site is at the bottom of the groove part. Four of the five conserved residues in the DnaQ superfamily within ExoI are acidic and can bind two metal ions[26]. Comparing to the other protein in DnaQ superfamily, Klenow fragment (KF) which is the large protein fragment cleaved from DNA polymerase I of E. coli., ExoI substitutes the Tyr 497 with His 181 which is the presumed to help the alignment of the nucleotides for hydrolysis. According to the similarity, the hydrolysis of ExoI is assumed to happen by attacking the scissile phosphate with one activated water molecule[26]. The extended loop region will enclose the DNA part and overlap the groove part[20]. The 3’ end of ssDNA is bound in the active site and the downstream end under the crossover loop. The middle part of the DNA is going to form a bulge, which approach the SH3-like domain, and the downstream end of the DNA form extensive interactions with an anchor site[25].


Functional structure

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In the middle of ExoI, there is a positive-charged groove with the nuclease active site at the bottom end. At the same site, one loop is bridging the SH3-like domain with C-terminal domains which overlaps through the top. The size of this groove can accommodate ∼12–13 nucleotides of ssDNA, which is compatible to the released product from previous literature[27][28].

References

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  1. ^ Blakesley RW, Dodgson JB, Nes IF, Wells RD (October 1977). "Duplex regions in "single-stranded" phiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegyptius". The Journal of Biological Chemistry. 252 (20): 7300–6. PMID 71298.
  2. ^ Kelley RB, Atkinson MR, Huberman JA, Kornberg A (1969). "Excision of thymine dimers and other mismatched sequences by DNA polymerases of Escherichia coli". Nature. 224: 495–501. doi:10.1038/224495a0.
  3. ^ Lehman IR, Nussbaum AL (August 1964). "The deoxyribonucleases of Escherichia coli. V. On the specificity of exonuclease I (phosphodiesterase)". The Journal of Biological Chemistry. 239: 2628–36. PMID 14235546.
  4. ^ a b c Breyer, Wendy A.; Matthews, Brian W. (2000-12). "Structure of Escherichia coli exonuclease I suggests how processivity is achieved". Nature Structural Biology. 7 (12): 1125–1128. doi:10.1038/81978. ISSN 1545-9985. {{cite journal}}: Check date values in: |date= (help)
  5. ^ "Abbexa - Antibodies, Proteins, ELISA kits". Abbexa. Retrieved 2022-09-30.
  6. ^ "ExPASy - ENZYME". enzyme.expasy.org. Retrieved 2022-09-30.
  7. ^ a b c Lehman, I.R.; Nussbaum, A.L. (1964-08). "The Deoxyribonucleases of Escherichia coli". Journal of Biological Chemistry. 239 (8): 2628–2636. doi:10.1016/s0021-9258(18)93898-6. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)
  8. ^ a b Lehman, I.R. (1960-05). "The Deoxyribonucleases of Escherichia coli". Journal of Biological Chemistry. 235 (5): 1479–1487. doi:10.1016/s0021-9258(18)69431-1. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)
  9. ^ Derbyshire, Victoria; Pinsonneault, Julia K.; Joyce, Catherine M. (1995-01-01), "[28] Structure-function analysis of 3′ → 5′-exonuclease of DNA polymerases", Methods in Enzymology, DNA Replication, vol. 262, Academic Press, pp. 363–385, doi:10.1016/0076-6879(95)62030-3, retrieved 2022-09-30
  10. ^ a b c Lovett, Susan T. (2011-06-09). Lovett, Susan T. (ed.). "The DNA Exonucleases of Escherichia coli". EcoSal Plus. 4 (2): ecosalplus.4.4.7. doi:10.1128/ecosalplus.4.4.7. ISSN 2324-6200. PMC 4238392. PMID 26442508.{{cite journal}}: CS1 maint: PMC format (link)
  11. ^ Kuzminov, Andrei (1999-12). "Recombinational Repair of DNA Damage in Escherichia coli and Bacteriophage λ". Microbiology and Molecular Biology Reviews. 63 (4): 751–813. doi:10.1128/MMBR.63.4.751-813.1999. ISSN 1092-2172. {{cite journal}}: Check date values in: |date= (help)
  12. ^ academic.oup.com. doi:10.1093/genetics/142.2.333 https://academic.oup.com/genetics/article/142/2/333/6016655. Retrieved 2022-10-23. {{cite web}}: Missing or empty |title= (help)
  13. ^ academic.oup.com. doi:10.1093/genetics/140.4.1175 https://academic.oup.com/genetics/article/140/4/1175/6013376. Retrieved 2022-10-23. {{cite web}}: Missing or empty |title= (help)
  14. ^ academic.oup.com. doi:10.1093/nar/20.18.4699 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/20.18.4699. Retrieved 2022-10-23. {{cite web}}: Missing or empty |title= (help)
  15. ^ Malgorzata, Bzymek. "Slipped Misalignment Mechanisms of Deletion Formation: In Vivo Susceptibility to Nucleases". Journal of Bacteriology. 181 (2): 477–482.
  16. ^ academic.oup.com. doi:10.1093/genetics/149.1.7 https://academic.oup.com/genetics/article/149/1/7/6034218. Retrieved 2022-10-23. {{cite web}}: Missing or empty |title= (help)
  17. ^ Smith, J; Modrich, P (1996-04-30). "Mutation detection with MutH, MutL, and MutS mismatch repair proteins". Proceedings of the National Academy of Sciences. 93 (9): 4374–4379. doi:10.1073/pnas.93.9.4374. ISSN 0027-8424. PMC 39545. PMID 8633074.{{cite journal}}: CS1 maint: PMC format (link)
  18. ^ a b Lahue, R. S.; Au, K. G.; Modrich, P. (1989-07-14). "DNA Mismatch Correction in a Defined System". Science. 245 (4914): 160–164. doi:10.1126/science.2665076. ISSN 0036-8075.
  19. ^ Burdett, Vickers; Baitinger, Celia; Viswanathan, Mohan; Lovett, Susan T.; Modrich, Paul (2001-06-05). "In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair". Proceedings of the National Academy of Sciences. 98 (12): 6765–6770. doi:10.1073/pnas.121183298. ISSN 0027-8424. PMC 34427. PMID 11381137.{{cite journal}}: CS1 maint: PMC format (link)
  20. ^ a b Su, S S; Lahue, R S; Au, K G; Modrich, P (1988-05). "Mispair specificity of methyl-directed DNA mismatch correction in vitro". Journal of Biological Chemistry. 263 (14): 6829–6835. doi:10.1016/s0021-9258(18)68718-6. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)
  21. ^ Qiu, Ruoyi; Sakato, Miho; Sacho, Elizabeth J.; Wilkins, Hunter; Zhang, Xingdong; Modrich, Paul; Hingorani, Manju M.; Erie, Dorothy A.; Weninger, Keith R. (2015-09). "MutL traps MutS at a DNA mismatch". Proceedings of the National Academy of Sciences. 112 (35): 10914–10919. doi:10.1073/pnas.1505655112. ISSN 0027-8424. PMC 4568282. PMID 26283381. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  22. ^ a b Grilley, M; Welsh, K M; Su, S S; Modrich, P (1989-01). "Isolation and Characterization of the Escherichia coli mutL Gene Product". Journal of Biological Chemistry. 264 (2): 1000–1004. doi:10.1016/s0021-9258(19)85043-3. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)
  23. ^ Cooper, D.L.; Lahue, R.S.; Modrich, P. (1993-06). "Methyl-directed mismatch repair is bidirectional". Journal of Biological Chemistry. 268 (16): 11823–11829. doi:10.1016/S0021-9258(19)50274-5. {{cite journal}}: Check date values in: |date= (help)
  24. ^ Burdett, Vickers; Baitinger, Celia; Viswanathan, Mohan; Lovett, Susan T.; Modrich, Paul (2001-06-05). "In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair". Proceedings of the National Academy of Sciences. 98 (12): 6765–6770. doi:10.1073/pnas.121183298. ISSN 0027-8424. PMC 34427. PMID 11381137.{{cite journal}}: CS1 maint: PMC format (link)
  25. ^ a b academic.oup.com. doi:10.1093/nar/gkt278. PMC 3675492. PMID 23609540 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt278. Retrieved 2022-09-30. {{cite web}}: Missing or empty |title= (help)CS1 maint: PMC format (link)
  26. ^ a b Beese, L. S.; Steitz, T. A. (1991-01). "Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism". The EMBO Journal. 10 (1): 25–33. doi:10.1002/j.1460-2075.1991.tb07917.x. {{cite journal}}: Check date values in: |date= (help)
  27. ^ Brody, Richard S. (1991-07-23). "Nucleotide positions responsible for the processivity of the reaction of exonuclease I with oligodeoxyribonucleotides". Biochemistry. 30 (29): 7072–7080. doi:10.1021/bi00243a006. ISSN 0006-2960.
  28. ^ Brody, R S; Doherty, K G; Zimmerman, P D (1986-06). "Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides". Journal of Biological Chemistry. 261 (16): 7136–7143. doi:10.1016/S0021-9258(17)38366-7. {{cite journal}}: Check date values in: |date= (help)
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