DNA repair protein human endonuclease VIII-like 1 (NEIL1)

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DNA repair protein human endonuclease VIII-like 1 (NEIL1)

Human Neil1
Human Neil1


Human NEI endonuclease complex with TRIS buffer, 1tdh
Ligands:
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml











Human Neil1 is a base-excision DNA repair protein which shows preference for repairing oxidation products of 8-oxoguanine. It is part of the base-excision repair system, which consists of families of proteins that protect the genome against endogenous and exogenous damages by repairing damaged DNA.

This structure consists of two domains connected by a , with an , and . Including a H2TH motif. (1tdh)[1]

DNA Repair and Base Excision DNA Repair

For a video of DNA repair click here. The picture below also illustrates DNA repair: Image:DNARepair.png The genome of any living organisms is being continuously affected by exogenous and endogenous agents, such as ultraviolet light, ionizing radiation, different chemicals and the cell's own metabolites (such as reactive oxygen). Therefore, different systems have evolved to repair these damages. With some of these systems shared throughout all lifeforms. Therefore, the proper functioning of DNA repair is critical for survival. There are six pathways of DNA repair (reviewed in Friedberg et al), and one of the is base-excision repair. The latter's distinguishing feature is that it removes lesions as single bases, as opposed to dNMPs or short oligonucleotides like other systems. [2]

Base excision repair's signature enzyme are the DNA glycosylases. These enzymes work by recognizing and removing a single damaged base from DNA. They are called DNA glycosylases because they hydrolize the N-glycosidic bond of the damaged deoxynucleoside. The subsequent steps of the pathway (strand incision, gap-filling and ligation) are done by other enzymes. See below for a cartoon of the process [3][4]:

Evolution and related structures

Cartoon phylogenetic tree of the FpgNei protein family.  Neil1 is one among several metazoan repair proteins
Cartoon phylogenetic tree of the FpgNei protein family. Neil1 is one among several metazoan repair proteins
Neil1 is part of the FpgNei superfamily of base excision repair proteins. And its one of 3 DNA glycosylases present in vertebrates, and in humans in particular. The evolution of this superfamily is not totally clear.

Homologous structures have been solved, including Fpg protein from Lactococcus Lactis (1pjj)[5], Bacillus Stereothermophilus (1r2y)[6], Thermos Thermophilus (1ee8)[7] and Escherichia Coli(1k82)[8] and Nei from Escherichia Coli (1k3w)[9]. The overall structure is similar, and some of the damages include 8-oxoguanine and fapyG (1xc8)[10].

Population variants can be found in hapmap project.

Human Neil1 Function

Role in Base excision repair

Guanine get oxidized to 8-oxoguanine, which in turn can get further oxidized in Sp and Gh.  This is a source of mutagenesis in the body
Guanine get oxidized to 8-oxoguanine, which in turn can get further oxidized in Sp and Gh. This is a source of mutagenesis in the body

Neil1 has as preferred substrate oxidation products of 8-Oxoguanine: spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). [11][12]. 8-oxoG produces hight levels of G:C → T:A transversion mutations in mammalian and bacterial cells [13][14]. In turn, site-specific oxidation of 8-oxoG can lead to the lesions Gh/Ia and Sp, leading to even higher G → T and G → C transversions. [15][16][17]

Localization and Expression

Human Neil1 is localized in the centrosomes and in the condensed chromosomes during mitosis[18]. Furthermore, given that there is another protein with overlapping substrate specificity and that Neil1 seems to act very well on bubble substrates, it has been suggested that Neil1 is active during replication and/or transcription [19].

Medical Implications

8-Oxoguanine can become oxidized to form Sp and Gh and actually show enhanced base misincorporation over the parent 8-oxoG lesion leading to G->T and G->C transversion mutations and thus stall polymerase. Double mouse knockouts of Neil1 and Nth (Nth1(-/-)Neil1(-/-)) show higher incidence of tumors than normal mice [20]. Furthermore, in both mice and humans there is evidence of Neil1 defficiency associated with metabolic syndrome [21][22]

Human Neil1 Structure

Overal Structure

This structure consists of two domains connected by a , with an , including a and an antiparallel β-hairpin zinc finger motifs [23][24].

Human Neil1 G. Stereothermophilus Fpg

Human Neil-1. Hinge peptide shown in red (PDB code 1tdh)

Bacterial Fpg complex with DNA (orange), 8-oxoguanine and Zn+2 ion (PDB code 1r2y)

DNA Binding

Other substrate-bound homologs have many interactions between DNA and protein, including the highly conserved and the . Neil1 has both the and a , an equivalent structural feature that does not bind zinc.[25][26]. This link has weblogos for the H2TH region

Substrate Recognition

Given its sequence homology, we expect Neil1 to works like other glycosylases, and . The actual recognition is still a mystery, but a bacterial homolog (with different substrate specificity) works as follows. An which inserts into the space left by the excised base. A plays a key role in substrate recognition. Discrimination between a guanine and 8-oxoG might be obtained by the altered protonation state of N7 and an .[27]

However, in human Neil1, this recognition complex is absent and a takes its place.[28]

Catalysis

The usual mode of catalysis for members of this family starts with a nucleophilic attack from the N-terminal amino group of are involved in the process ( in Fpg). Several subsequent mechanisms have been proposed.[29][30][31] A good illustration can be found in Gilboa et al.[32].

Known Mutations

P2,K56,R248 in E. Coli are known to inactivate the enzyme [33][34].

Helix Capping and Pi-Cation Interactions

Helix Ncapping Ccapping

References

  1. Doublie S, Bandaru V, Bond JP, Wallace SS. The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10284-9. Epub 2004 Jul 1. PMID:15232006 doi:10.1073/pnas.0402051101
  2. Zharkov DO. Base excision DNA repair. Cell Mol Life Sci. 2008 May;65(10):1544-65. PMID:18259689 doi:10.1007/s00018-008-7543-2
  3. Zharkov DO. Base excision DNA repair. Cell Mol Life Sci. 2008 May;65(10):1544-65. PMID:18259689 doi:10.1007/s00018-008-7543-2
  4. Robertson AB, Klungland A, Rognes T, Leiros I. DNA repair in mammalian cells: Base excision repair: the long and short of it. Cell Mol Life Sci. 2009 Mar;66(6):981-93. PMID:19153658 doi:10.1007/s00018-009-8736-z
  5. Pereira de Jesus K, Serre L, Zelwer C, Castaing B. Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA. Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784 doi:http://dx.doi.org/33/18/5936
  6. Fromme JC, Verdine GL. DNA lesion recognition by the bacterial repair enzyme MutM. J Biol Chem. 2003 Dec 19;278(51):51543-8. Epub 2003 Oct 1. PMID:14525999 doi:10.1074/jbc.M307768200
  7. Sugahara M, Mikawa T, Kumasaka T, Yamamoto M, Kato R, Fukuyama K, Inoue Y, Kuramitsu S. Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. EMBO J. 2000 Aug 1;19(15):3857-69. PMID:10921868 doi:http://dx.doi.org/10.1093/emboj/19.15.3857
  8. Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217 doi:http://dx.doi.org/10.1074/jbc.M202058200
  9. Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G. Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. EMBO J. 2002 Feb 15;21(4):789-800. PMID:11847126 doi:10.1093/emboj/21.4.789
  10. Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B. Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase. J Biol Chem. 2004 Oct 15;279(42):44074-83. Epub 2004 Jul 10. PMID:15249553 doi:10.1074/jbc.M405928200
  11. Hailer MK, Slade PG, Martin BD, Rosenquist TA, Sugden KD. Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2. DNA Repair (Amst). 2005 Jan 2;4(1):41-50. PMID:15533836 doi:10.1016/j.dnarep.2004.07.006
  12. Krishnamurthy N, Zhao X, Burrows CJ, David SS. Superior removal of hydantoin lesions relative to other oxidized bases by the human DNA glycosylase hNEIL1. Biochemistry. 2008 Jul 8;47(27):7137-46. Epub 2008 Jun 11. PMID:18543945 doi:10.1021/bi800160s
  13. Grollman AP, Moriya M. Mutagenesis by 8-oxoguanine: an enemy within. Trends Genet. 1993 Jul;9(7):246-9. PMID:8379000
  14. 1461734
  15. Muller JG, Duarte V, Hickerson RP, Burrows CJ. Gel electrophoretic detection of 7,8-dihydro-8-oxoguanine and 7, 8-dihydro-8-oxoadenine via oxidation by Ir (IV). Nucleic Acids Res. 1998 May 1;26(9):2247-9. PMID:9547288
  16. Leipold MD, Muller JG, Burrows CJ, David SS. Removal of hydantoin products of 8-oxoguanine oxidation by the Escherichia coli DNA repair enzyme, FPG. Biochemistry. 2000 Dec 5;39(48):14984-92. PMID:11101315
  17. Henderson PT, Delaney JC, Gu F, Tannenbaum SR, Essigmann JM. Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in vivo. Biochemistry. 2002 Jan 22;41(3):914-21. PMID:11790114
  18. Hildrestrand GA, Rolseth V, Bjoras M, Luna L. Human NEIL1 localizes with the centrosomes and condensed chromosomes during mitosis. DNA Repair (Amst). 2007 Oct 1;6(10):1425-33. Epub 2007 Jun 6. PMID:17556049 doi:10.1016/j.dnarep.2007.04.008
  19. Hazra TK, Das A, Das S, Choudhury S, Kow YW, Roy R. Oxidative DNA damage repair in mammalian cells: a new perspective. DNA Repair (Amst). 2007 Apr 1;6(4):470-80. Epub 2006 Nov 20. PMID:17116430 doi:10.1016/j.dnarep.2006.10.011
  20. Chan MK, Ocampo-Hafalla MT, Vartanian V, Jaruga P, Kirkali G, Koenig KL, Brown S, Lloyd RS, Dizdaroglu M, Teebor GW. Targeted deletion of the genes encoding NTH1 and NEIL1 DNA N-glycosylases reveals the existence of novel carcinogenic oxidative damage to DNA. DNA Repair (Amst). 2009 Jul 4;8(7):786-94. Epub 2009 Apr 5. PMID:19346169 doi:10.1016/j.dnarep.2009.03.001
  21. Roy LM, Jaruga P, Wood TG, McCullough AK, Dizdaroglu M, Lloyd RS. Human polymorphic variants of the NEIL1 DNA glycosylase. J Biol Chem. 2007 May 25;282(21):15790-8. Epub 2007 Mar 26. PMID:17389588 doi:10.1074/jbc.M610626200
  22. Vartanian V, Lowell B, Minko IG, Wood TG, Ceci JD, George S, Ballinger SW, Corless CL, McCullough AK, Lloyd RS. The metabolic syndrome resulting from a knockout of the NEIL1 DNA glycosylase. Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1864-9. Epub 2006 Jan 30. PMID:16446448
  23. Wallace SS, Bandaru V, Kathe SD, Bond JP. The enigma of endonuclease VIII. DNA Repair (Amst). 2003 May 13;2(5):441-53. PMID:12713806
  24. Zharkov DO, Rieger RA, Iden CR, Grollman AP. NH2-terminal proline acts as a nucleophile in the glycosylase/AP-lyase reaction catalyzed by Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg) protein. J Biol Chem. 1997 Feb 21;272(8):5335-41. PMID:9030608
  25. Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217 doi:http://dx.doi.org/10.1074/jbc.M202058200
  26. Paksoy Y, Vatansev H, Seker M, Ustun ME, Buyukmumcu M, Akpinar Z. Congenital morphological abnormalities of the distal vertebral arteries (CMADVA) and their relationship with vertigo and dizziness. Med Sci Monit. 2004 Jul;10(7):CR316-23. Epub 2004 Jun 29. PMID:15232506
  27. Fromme JC, Banerjee A, Huang SJ, Verdine GL. Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature. 2004 Feb 12;427(6975):652-6. PMID:14961129 doi:10.1038/nature02306
  28. Doublie S, Bandaru V, Bond JP, Wallace SS. The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10284-9. Epub 2004 Jul 1. PMID:15232006 doi:10.1073/pnas.0402051101
  29. Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G. Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. EMBO J. 2002 Feb 15;21(4):789-800. PMID:11847126 doi:10.1093/emboj/21.4.789
  30. Sugahara M, Mikawa T, Kumasaka T, Yamamoto M, Kato R, Fukuyama K, Inoue Y, Kuramitsu S. Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. EMBO J. 2000 Aug 1;19(15):3857-69. PMID:10921868 doi:http://dx.doi.org/10.1093/emboj/19.15.3857
  31. Pereira de Jesus K, Serre L, Zelwer C, Castaing B. Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA. Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784 doi:http://dx.doi.org/33/18/5936
  32. Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217 doi:http://dx.doi.org/10.1074/jbc.M202058200
  33. Golan G, Zharkov DO, Feinberg H, Fernandes AS, Zaika EI, Kycia JH, Grollman AP, Shoham G. Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Nucleic Acids Res. 2005 Sep 6;33(15):5006-16. Print 2005. PMID:16145054 doi:http://dx.doi.org/33/15/5006
  34. Burgess S, Jaruga P, Dodson ML, Dizdaroglu M, Lloyd RS. Determination of active site residues in Escherichia coli endonuclease VIII. J Biol Chem. 2002 Jan 25;277(4):2938-44. Epub 2001 Nov 15. PMID:11711552 doi:10.1074/jbc.M110499200

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