User:Ramiro Barrantes/FpgNeiRepair

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Contents

The FpgNei Protein Superfamily

Background on DNA Repair

The genome of any living organism is 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), which include 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. [1]

Base excision repair's signature enzyme are the DNA glycosylases. These enzymes work by recognizing a damaged base, and then hydrolizing the N-glycosidic bond of the damaged deoxynucleoside and thus removing a single damaged base from DNA. The subsequent steps of the pathway (strand incision, gap-filling and ligation) are done by other enzymes. [2][3]

Background on Fpg Nei

Overall Function and Structure

(For FPG, the structure used was 1r2y and for Nei 1k3w) Members of this family have . When enzyme binds to DNA, the damaged base

. This superfamily is also characterized by containing a ; as well as a . Both the H2TH motif and the Zinc finger, as well as other residues . [4]. Catalysis is believed to be mediated by . For information on the mechanism please consult [5][6][7][8][9].

Similarly In EcoNei (structure 1k3w, , and (Thymine Glycol in the case of Nei). [10]. Some of these amino acids are stabilized by a (although a zincless finger motif is present in some of these subfamilies [11]). Analogously to Fpg, ), Note that the last two elements discussed, the zinc vs. zincless finger, and the two kinds of intercalation loops, are examples of coevolving functional clusters, groups of amino acids that perform a function, and that might be unnecessary or compensated for within the other subfamilies. We developed a novel method for identifying these clusters and have applied it to bring insight into the structure, function and evolution FpgNei family.

See structure column for structure reference

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Cartoon phylogenetic tree of the FpgNei protein family. Note that this phylogeny can be appreciated in two levels: by the distribution and number of FpgNei subfamilies in different organisms; and by the kinds of damages that can be repaired
Cartoon phylogenetic tree of the FpgNei protein family. Note that this phylogeny can be appreciated in two levels: by the distribution and number of FpgNei subfamilies in different organisms; and by the kinds of damages that can be repaired
Clade Function References
Fpg 8oxoG, Fapy-A, Fapy-G,Me-Fapy-G,Sp,Gh [12][13]
EcoNei Oxidized pyrimidines [14]
Actinomycetes Nei1 DHU [15]
Actinomycetes Nei2  ?
Fpg2  ?
Plant&Fungi Sp,Gh [16]
Neil1 Sp,Gh,on double&single strand DNA [17]
Neil2 Sp,Gh,on double&single stranded DNA [18]
Neil3 not clear [19]

Several authors have suggested mechanisms for these enzymes, please see references for more information [20][21][22][23].

Homologous structures have been solved, including Fpg protein from Lactococcus Lactis (1pjj)[24], Bacillus Stereothermophilus (1r2y)[25], Thermos Thermophilus (1ee8)[26] and Escherichia Coli(1k82)[27] and Nei from Escherichia Coli (1k3w)[28]. The overall structure is similar, and some of the damages include 8-oxoguanine and fapyG (1xc8)[29].

Latent Structural Characters (LSCs)

We define a latent structural character (LSC) as neighboring amino acids which have changed in rate or constraint for a given clade or set of clades. For example, the cysteines in the zinc finger are all conserved in the fpg1, fpg2, actinobacterial and eukaryotic clades, but have a higher rate in plants and neil1, as the latter have a zinc-less finger (see here for more information). We developed a novel method to find these groups of amino acids, discovering previously unknown groups of amino acids which are functionally important in some of these subfamilies.

The table below has some of our main findings, there are two variants for each LSC in case that for one LSC there is a compensating cluster in the other subfamilies. If you click on one of them you will see the result in the structure, and you can go to the explanation and the sequence distribution below.
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LSC1: Stability of perfectly conserved Asn168

WebLogo for the first functional unit, note the equivalent roles between lysine and arginine, which hydrogen-bond with the crucial Asn174
WebLogo for the first functional unit, note the equivalent roles between lysine and arginine, which hydrogen-bond with the crucial Asn174
( and ). Asn174 (in yellow), part of the helix-two-turn-helix (H2TH) domain (in orange), along with two other amino acids (including the key amino acid Arg264, in yellow) have an effect in the orientation and kinking of the DNA [30]. Both the H2TH and the zinc finger are the two DNA binding motifs of FpgNei [31]. In 4 of the 9 clades (Fpg1, Fpg2 and Plants and Fungi) we hypothesize that Asn174 is stabilized by the amino acid corresponding to Lys160, which in turn hydrogen bonds with Thr266 and Gly265. In GstFpg, Lys160 helps keep the proper arrangement between the zinc finger (in blue) and the H2TH (in beige) [32]. In the other subfamilies (Actinobacteria 1 and 2, Proteobacteria and all vertebrate subfamilies), this role is played by Arg171, which originates on a different helix, and hydrogen bonds to the other beta-sheet of the zinc-finger. Site directed mutagenesis on Lys155 (corresponding lysine in E. coli Fpg) and on Arg171 result in premature dissociation and/or loss of activity [33][34]. Our analysis revealed the possible compensatory role of both LSCs as well as hypotheses on other residues which might be important to stabilize Asn174.

PDB ID 1R2Y

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PDB ID 1K3W

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LSC2: Stability of catalytic helix

( and )

The LER triad interact and might stabilize the catalytic helix (which includes Pro2 and Glu3 and Glu6), it is not clear how this is achieved in the other subfamilies
The LER triad interact and might stabilize the catalytic helix (which includes Pro2 and Glu3 and Glu6), it is not clear how this is achieved in the other subfamilies
The triad Leu4, Glu8 and Arg57 is highly conserved in fpg1, fpg2, and plants and fungi. However, the role of these group of amino acids has not been discussed in the literature. Site directed mutagenesis has been performed on Arg57, resulting in reduced binding [35] (glycosylase activity was not measured). We entertain two hypotheses about the role of this triad: perhaps this group of amino acids stabilizes helixA (brown), which contains the catalytic residues Pro2,Glu3 and Glu6 [36][37]. Another possible role is in contributing to the stability of Lys60, key for glycosylase and lyase activity, and thus with the other LSC related to the stability of site Lys60. The key interaction for this role corresponds to the highly conserved Glu137 (yellow), which when mutated results in 20-fold decrease in activity in EcoNei[38][39]). However, the corresponding amino acid in E. coli (D128) does not affect activity after mutated[40]. Please see next LSC for more information. Therefore, our analysis shed light on an unstudied group of cooperating amino acids which might be important for function.

PDB ID 1R2Y

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PDB ID 1K3W

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LSC3: Neil1-specific: Stability of Lys60

Notice the covariation in Neil1 and the rest with positions 134 and 137 and 170
Notice the covariation in Neil1 and the rest with positions 134 and 137 and 170
( and ) Gly59 and Lys60 (yellow) are important in the activity of MutM [41][42] (reflected by their perfect conservation). Lys60 interacts with the the 3' phosphate of 8oxoG [43]. Our analysis revealed a site (Glu137) which is the main hydrogen bond with Gly59. Mutation of this site in Fpg results in 20-fold decrease in activity[44][45]. In Fpg, Plants and Fungi, this LSC could be related to the triad Leu4/Glu8/Arg57. Glu/Asp 137 is present in all clades except Neil1, however, in . This amino acid is compensated for by Asn172 in Neil1 (in green). Therefore, Our analysis showed a key amino acid which has been compensated for in a differnet clade for Asn172, however, it came up as part of a network to other important amino acids. It is interesting that Glu137 was replaced by a cysteine (Cys136) in Neil1.

PDB ID 1R2Y

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PDB ID 1TDH

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LSC4: Intercalation Loop

and )

The residue in positions 77 and 78 suggest a possible intercalation loop
The residue in positions 77 and 78 suggest a possible intercalation loop
The intercalation loop (green) inserts into the space left by the excised base. This structure, as well as a group of amino acids that support it (also in green) exhibit high conservation in Fpg, AY, plants and Neil1, whereas the other have a higher substitution rate in the corresponding amino acid, while containing the methionine (yellow). The best studied example is its counterpart is in E. coli Nei, which fulfills the same purpose as the Fpg intercalation loop [46], by inserting into the DNA when the base is everted. Note that the amino acid composition suggests that mimivirus has this structure.

PDB ID 1R2Y

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PDB ID 1K3W

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LSC5: DNA Binding Tyrosine

Tyrosine that binds to DNA, plants have a different structure alltogether
Tyrosine that binds to DNA, plants have a different structure alltogether

This tyrosine hydrogen bonds with Glu179 (BstFpg coordinates). Glu179 is perfectly conserved throughout all clades, and its mutation results in loss of activity [47]. We find that this Tyrosine is replaced by an arginine in plants, however, this arginine could be fulfilling the same role as the tyrosine and might not account for any difference in function. This is consistent with Glu179 and Tyr243 being part of the same network and for Tyr243 playing an important role in the function of the protein. However, this amino acid hasn't been studied. On the other hand, Arg244 is very hightly conserved in everything but Neil1 and plants, consistent with the idea that it might contribute to Zinc Finger stability. The presence of Arg244 correlates with the presence of Pro248, which is the amino acid right before Cys249, which holds the Zinc.

PDB ID 1R2Y

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LSC6: Zinc/zincless finger

The Zinc Finger helps as a support of the key R264 residue
The Zinc Finger helps as a support of the key R264 residue
and

The Zinc finger (of the β/β-antiparallel CCCC type) serves to hold the absolutely conserved Arg264 residue [48], which binds to the phosphate of the damaged base and is crucial for function (mutation of this site results in failed cleavage of the damaged base [49]). Site directed mutagenesis experiments have been performed on all four cysteines, leading to loss of activity [50][51], emphasizing the importance of this LSC. In Neil1, there is no Zinc but there is an equivalent structure: a "zincless finger" [52]. Both the plants and mimivirus have a zincless finger as well [53][54], although it is not clear if these are all homologous.

PDB ID 1R2Y

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PDB ID 1TDH

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PDB ID 1R2Y

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PDB ID 1K3W

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Functional Cluster Variant 1 Variant 2 Fpg1 Fpg2 Plant Neil1 Neil2 Neil3 Proteo Actino1 Actino2 MimiVirus
Support for perfectly conserved Asn174 1 1 1 0 0 0 0 0 0 0
Stability of catalytic helix 1 1 1 - - - - - - -
Neil1-specific: Stability of Lys60 Y Y Y N Y Y Y Y Y Y
Intercalation loop Y Y Y N N N N N N Y
PlantFungi-specific: R254 DNA binding different in plants Y Y N Y Y Y N Y Y Y
Zinc Finger Y Y N N Y Y Y Y Y N
Recognition complex none Y N N N N N N N N N


LSC7: Recognition Complex

This complex is key in recognizing damaged guanine, in the literature it is referred to as the alpha10-b9 loop. For details and hypothesis on the structural basis of 8oxoG and fapyG recognition please refer to [55][56]. The area corresponding to this complex is much shorter in some of the other subfamilies, and there is no obvious homology. In the EcoNei and Neil1 structures this loop is absent as well [57][58]. We showed that the distribution of the rates of substitution within this loop is non-random, providing further support for the importance of the loop in the specificity in Fpg. This non-randomness is also present in 3 of the other subfamilies perhaps suggesting a possible important role of this area in those subfamilies.

Zinc/zincless finger

Tyrosine that binds to DNA, the plant has a different structure alltogether
Tyrosine that binds to DNA, the plant has a different structure alltogether

Evolution

The FpgNei evolution has not been easy to resolve [59], especially in the deeper branches. Assuming that functional clusters evolve more slowly than individual residues, we can use this as phylogenetic characters to 1) draw the most parsimonious evolution of the superfamily as dictated by these functional clusters 2) examine how these clusters have evolved and how this might have influenced the evolution of FpgNei. Image:Scenario1.png

Site-directed mutants

The following we intend to be comprehensive list of site-directed mutants from the literature. The description is just a very brief, and thus inaccurate summary. Please see the relevant reference for more information on assays used and precise results.

Name Organism/Structure Effect Reference
E. coli Nei (1k3w) Inactive but can still make Schiff Base. [60][61][62][63]
E. coli Nei (1k3w) inactive [64][65]
E. coli Nei (1k3w) Decrease glycosylase, lyase ok. [66]
E. coli Nei (1k3w) Decrease glycosylase, lyase ok. [67]
E. coli Fpg (1k82) No activity. [68]
E. coli Nei (1k3w) No change. [69]
E. coli Fpg (1k82) 3-fold decreased activity. [70][71]
E. coli Fpg (1k82) higher Kd (reduced binding) [72]
E. coli Fpg (1k82) higher Kd (reduced binding) [73]
E. coli Fpg (1k82) similar activity[74]
E. coli Fpg (1k82) reduced glygosylase, less efficient in Schiff-base complex. No cleavage. [75][76][77][78][79]
E. coli Fpg (1k82) similar activity but reduced turnover on 8oxoG:C[80]
B. stereo Fpg (1r2y) Switches preferences for syn and anti in 8oxoG [81]
E. coli Nei (1k3w) Decreased or no activity [82]
E. coli Fpg (1k82) reduced rate of excision [83]
E. coli Nei (1k3w) Active but different kinetics. [84]
E. coli Fpg (1k82) No change. [85]
E. coli Fpg (1k82) Abolished binding [86]
E. coli Fpg (1k82) Decreases processivity [87]
E. coli Nei (1k3w) same [88]
E. coli Fpg (1k82) 20-fold decreased activity. [89][90]
E. coli Fpg (1k82) reduced glygosylase, less efficient in Schiff-base complex. No cleavage. [91][92]
E. coli Nei (1k3w) same [93]
E. coli Fpg (1k82) same [94]
E. coli Nei (1k3w) reduced activity, loss of opposite base discrimination [95]
E. coli Nei (1k3w) ok lyase, reduced glycosylase [96]
E. coli Fpg (1k82) No activity. [97]
E. coli Nei (1k3w) Decreased activity on 5S,6R Tg, slightly less active on DHU [98]
B. stereo Fpg (1r2y) Selectively reduced excision ability [99]
E. coli Nei (1k3w) inactive, although can cleave AP sites [100]
H. Sapiens Neil1 (1tdh) Low activity [101]
E. coli Fpg (1k82) No binding nor cleavage [102]
E. coli Fpg (1k82) No binding nor cleavage. No zinc, no altered secondary structure [103]
E. coli Nei (1k3w) Loss of activity [104]
E. coli Fpg (1k82) No lyase nor glycosylase [105]

See structure column for structure reference

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References

  1. ↑ 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
  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. ↑ 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
  4. ↑ 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
  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. ↑ 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
  7. ↑ 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
  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. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
  13. ↑ David SS, Williams SD. Chemistry of Glycosylases and Endonucleases Involved in Base-Excision Repair. Chem Rev. 1998 May 7;98(3):1221-1262. PMID:11848931
  14. ↑ Jiang D, Hatahet Z, Melamede RJ, Kow YW, Wallace SS. Characterization of Escherichia coli endonuclease VIII. J Biol Chem. 1997 Dec 19;272(51):32230-9. PMID:9405426
  15. ↑ Sidorenko VS, Rot MA, Filipenko ML, Nevinsky GA, Zharkov DO. Novel DNA glycosylases from Mycobacterium tuberculosis. Biochemistry (Mosc). 2008 Apr;73(4):442-50. PMID:18457574
  16. ↑ Kathe SD, Barrantes-Reynolds R, Jaruga P, Newton MR, Burrows CJ, Bandaru V, Dizdaroglu M, Bond JP, Wallace SS. Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases. DNA Repair (Amst). 2009 May 1;8(5):643-53. Epub 2009 Feb 12. PMID:19217358 doi:10.1016/j.dnarep.2008.12.013
  17. ↑ 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
  18. ↑ 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
  19. ↑ Takao M, Oohata Y, Kitadokoro K, Kobayashi K, Iwai S, Yasui A, Yonei S, Zhang QM. Human Nei-like protein NEIL3 has AP lyase activity specific for single-stranded DNA and confers oxidative stress resistance in Escherichia coli mutant. Genes Cells. 2009 Feb;14(2):261-70. Epub 2008 Jan 15. PMID:19170771 doi:10.1111/j.1365-2443.2008.01271.x
  20. ↑ 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
  21. ↑ 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
  22. ↑ 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
  23. ↑ 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
  24. ↑ 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
  25. ↑ 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
  26. ↑ 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
  27. ↑ 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
  28. ↑ 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
  29. ↑ 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
  30. ↑ 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
  31. ↑ 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
  32. ↑ 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
  33. ↑ Rabow L, Venkataraman R, Kow YW. Mechanism of action of Escherichia coli formamidopyrimidine N-glycosylase: role of K155 in substrate binding and product release. Prog Nucleic Acid Res Mol Biol. 2001;68:223-34. PMID:11554299
  34. ↑ Kropachev KY, Zharkov DO, Grollman AP. Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Biochemistry. 2006 Oct 3;45(39):12039-49. PMID:17002303 doi:10.1021/bi060663e
  35. ↑ Rogacheva M, Ishchenko A, Saparbaev M, Kuznetsova S, Ogryzko V. High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem. 2006 Oct 27;281(43):32353-65. Epub 2006 Aug 22. PMID:16928690 doi:10.1074/jbc.M606217200
  36. ↑ 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
  37. ↑ 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
  38. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  39. ↑ Perlow-Poehnelt RA, Zharkov DO, Grollman AP, Broyde S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry. 2004 Dec 28;43(51):16092-105. PMID:15610004 doi:10.1021/bi048747f
  40. ↑ 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
  41. ↑ Sidorkina OM, Laval J. Role of lysine-57 in the catalytic activities of Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg protein). Nucleic Acids Res. 1998 Dec 1;26(23):5351-7. PMID:9826758
  42. ↑ 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
  43. ↑ Rogacheva M, Ishchenko A, Saparbaev M, Kuznetsova S, Ogryzko V. High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem. 2006 Oct 27;281(43):32353-65. Epub 2006 Aug 22. PMID:16928690 doi:10.1074/jbc.M606217200
  44. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  45. ↑ Perlow-Poehnelt RA, Zharkov DO, Grollman AP, Broyde S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry. 2004 Dec 28;43(51):16092-105. PMID:15610004 doi:10.1021/bi048747f
  46. ↑ Kropachev KY, Zharkov DO, Grollman AP. Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Biochemistry. 2006 Oct 3;45(39):12039-49. PMID:17002303 doi:10.1021/bi060663e
  47. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  48. ↑ 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
  49. ↑ 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
  50. ↑ O'Connor TR, Graves RJ, de Murcia G, Castaing B, Laval J. Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. J Biol Chem. 1993 Apr 25;268(12):9063-70. PMID:8473347
  51. ↑ Tchou J, Michaels ML, Miller JH, Grollman AP. Function of the zinc finger in Escherichia coli Fpg protein. J Biol Chem. 1993 Dec 15;268(35):26738-44. PMID:8253809
  52. ↑ 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
  53. ↑ Kathe SD, Barrantes-Reynolds R, Jaruga P, Newton MR, Burrows CJ, Bandaru V, Dizdaroglu M, Bond JP, Wallace SS. Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases. DNA Repair (Amst). 2009 May 1;8(5):643-53. Epub 2009 Feb 12. PMID:19217358 doi:10.1016/j.dnarep.2008.12.013
  54. ↑ Bandaru V, Zhao X, Newton MR, Burrows CJ, Wallace SS. Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus. DNA Repair (Amst). 2007 Nov;6(11):1629-41. Epub 2007 Jul 12. PMID:17627905 doi:10.1016/j.dnarep.2007.05.011
  55. ↑ 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
  56. ↑ 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
  57. ↑ 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
  58. ↑ 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
  59. ↑ 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
  60. ↑ 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
  61. ↑ Kuznetsov SV, Sidorkina OM, Jurado J, Bazin M, Tauc P, Brochon JC, Laval J, Santus R. Effect of single mutations on the structural dynamics of a DNA repair enzyme, the Escherichia coli formamidopyrimidine-DNA glycosylase--a fluorescence study using tryptophan residues as reporter groups. Eur J Biochem. 1998 Apr 15;253(2):413-20. PMID:9654091
  62. ↑ Saparbaev M, Sidorkina OM, Jurado J, Privezentzev CV, Greenberg MM, Laval J. Repair of oxidized purines and damaged pyrimidines by E. coli Fpg protein: different roles of proline 2 and lysine 57 residues. Environ Mol Mutagen. 2002;39(1):10-7. PMID:11813291
  63. ↑ Sidorkina OM, Laval J. Role of the N-terminal proline residue in the catalytic activities of the Escherichia coli Fpg protein. J Biol Chem. 2000 Apr 7;275(14):9924-9. PMID:10744666
  64. ↑ 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
  65. ↑ 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
  66. ↑ 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
  67. ↑ 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
  68. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  69. ↑ 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
  70. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  71. ↑ Perlow-Poehnelt RA, Zharkov DO, Grollman AP, Broyde S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry. 2004 Dec 28;43(51):16092-105. PMID:15610004 doi:10.1021/bi048747f
  72. ↑ Rogacheva M, Ishchenko A, Saparbaev M, Kuznetsova S, Ogryzko V. High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem. 2006 Oct 27;281(43):32353-65. Epub 2006 Aug 22. PMID:16928690 doi:10.1074/jbc.M606217200
  73. ↑ Rogacheva M, Ishchenko A, Saparbaev M, Kuznetsova S, Ogryzko V. High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem. 2006 Oct 27;281(43):32353-65. Epub 2006 Aug 22. PMID:16928690 doi:10.1074/jbc.M606217200
  74. ↑ Rogacheva M, Ishchenko A, Saparbaev M, Kuznetsova S, Ogryzko V. High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem. 2006 Oct 27;281(43):32353-65. Epub 2006 Aug 22. PMID:16928690 doi:10.1074/jbc.M606217200
  75. ↑ Sidorkina OM, Laval J. Role of lysine-57 in the catalytic activities of Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg protein). Nucleic Acids Res. 1998 Dec 1;26(23):5351-7. PMID:9826758
  76. ↑ 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
  77. ↑ Kuznetsov SV, Sidorkina OM, Jurado J, Bazin M, Tauc P, Brochon JC, Laval J, Santus R. Effect of single mutations on the structural dynamics of a DNA repair enzyme, the Escherichia coli formamidopyrimidine-DNA glycosylase--a fluorescence study using tryptophan residues as reporter groups. Eur J Biochem. 1998 Apr 15;253(2):413-20. PMID:9654091
  78. ↑ Rogacheva M, Ishchenko A, Saparbaev M, Kuznetsova S, Ogryzko V. High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem. 2006 Oct 27;281(43):32353-65. Epub 2006 Aug 22. PMID:16928690 doi:10.1074/jbc.M606217200
  79. ↑ Saparbaev M, Sidorkina OM, Jurado J, Privezentzev CV, Greenberg MM, Laval J. Repair of oxidized purines and damaged pyrimidines by E. coli Fpg protein: different roles of proline 2 and lysine 57 residues. Environ Mol Mutagen. 2002;39(1):10-7. PMID:11813291
  80. ↑ Harbut MB, Meador M, Dodson ML, Lloyd RS. Modulation of the turnover of formamidopyrimidine DNA glycosylase. Biochemistry. 2006 Jun 13;45(23):7341-6. PMID:16752923 doi:10.1021/bi052383p
  81. ↑ Song K, Hornak V, de Los Santos C, Grollman AP, Simmerling C. Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase. Biochemistry. 2006 Sep 12;45(36):10886-94. PMID:16953574 doi:10.1021/bi060380m
  82. ↑ Kropachev KY, Zharkov DO, Grollman AP. Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Biochemistry. 2006 Oct 3;45(39):12039-49. PMID:17002303 doi:10.1021/bi060663e
  83. ↑ Zaika EI, Perlow RA, Matz E, Broyde S, Gilboa R, Grollman AP, Zharkov DO. Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis. J Biol Chem. 2004 Feb 6;279(6):4849-61. Epub 2003 Nov 7. PMID:14607836 doi:10.1074/jbc.M310262200
  84. ↑ Dizdaroglu M, Burgess SM, Jaruga P, Hazra TK, Rodriguez H, Lloyd RS. Substrate specificity and excision kinetics of Escherichia coli endonuclease VIII (Nei) for modified bases in DNA damaged by free radicals. Biochemistry. 2001 Oct 9;40(40):12150-6. PMID:11580290
  85. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  86. ↑ Zaika EI, Perlow RA, Matz E, Broyde S, Gilboa R, Grollman AP, Zharkov DO. Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis. J Biol Chem. 2004 Feb 6;279(6):4849-61. Epub 2003 Nov 7. PMID:14607836 doi:10.1074/jbc.M310262200
  87. ↑ Sidorenko VS, Zharkov DO. Correlated cleavage of damaged DNA by bacterial and human 8-oxoguanine-DNA glycosylases. Biochemistry. 2008 Aug 26;47(34):8970-6. Epub 2008 Aug 2. PMID:18672903 doi:10.1021/bi800569e
  88. ↑ 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
  89. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  90. ↑ Perlow-Poehnelt RA, Zharkov DO, Grollman AP, Broyde S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry. 2004 Dec 28;43(51):16092-105. PMID:15610004 doi:10.1021/bi048747f
  91. ↑ Rabow LE, Kow YW. Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis. Biochemistry. 1997 Apr 22;36(16):5084-96. PMID:9125531 doi:10.1021/bi963005a
  92. ↑ Rabow L, Venkataraman R, Kow YW. Mechanism of action of Escherichia coli formamidopyrimidine N-glycosylase: role of K155 in substrate binding and product release. Prog Nucleic Acid Res Mol Biol. 2001;68:223-34. PMID:11554299
  93. ↑ 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
  94. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  95. ↑ Kropachev KY, Zharkov DO, Grollman AP. Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Biochemistry. 2006 Oct 3;45(39):12039-49. PMID:17002303 doi:10.1021/bi060663e
  96. ↑ 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
  97. ↑ Lavrukhin OV, Lloyd RS. Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase. Biochemistry. 2000 Dec 12;39(49):15266-71. PMID:11106507
  98. ↑ 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
  99. ↑ Zaika EI, Perlow RA, Matz E, Broyde S, Gilboa R, Grollman AP, Zharkov DO. Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis. J Biol Chem. 2004 Feb 6;279(6):4849-61. Epub 2003 Nov 7. PMID:14607836 doi:10.1074/jbc.M310262200
  100. ↑ 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
  101. ↑ Shinmura K, Tao H, Goto M, Igarashi H, Taniguchi T, Maekawa M, Takezaki T, Sugimura H. Inactivating mutations of the human base excision repair gene NEIL1 in gastric cancer. Carcinogenesis. 2004 Dec;25(12):2311-7. Epub 2004 Aug 19. PMID:15319300 doi:10.1093/carcin/bgh267
  102. ↑ Tchou J, Michaels ML, Miller JH, Grollman AP. Function of the zinc finger in Escherichia coli Fpg protein. J Biol Chem. 1993 Dec 15;268(35):26738-44. PMID:8253809
  103. ↑ Tchou J, Michaels ML, Miller JH, Grollman AP. Function of the zinc finger in Escherichia coli Fpg protein. J Biol Chem. 1993 Dec 15;268(35):26738-44. PMID:8253809
  104. ↑ Kropachev KY, Zharkov DO, Grollman AP. Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Biochemistry. 2006 Oct 3;45(39):12039-49. PMID:17002303 doi:10.1021/bi060663e
  105. ↑ O'Connor TR, Graves RJ, de Murcia G, Castaing B, Laval J. Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. J Biol Chem. 1993 Apr 25;268(12):9063-70. PMID:8473347

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