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PDBsum entry 1k82

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1k82
Jmol
Contents
Protein chains
260 a.a. *
DNA/RNA
Metals
_ZN ×4
Waters ×499
* Residue conservation analysis
PDB id:
1k82
Name: Hydrolase/DNA
Title: Crystal structure of e.Coli formamidopyrimidine-DNA glycosylase (fpg) covalently trapped with DNA
Structure: 5'-d( Gp Gp Cp Tp Tp Cp Cp Tp Cp Cp Tp Gp G)-3'. Chain: e, f, g, h. Synonym: fapy-DNA glycosylase, fpg. Engineered: yes. 5'-d( Cp Cp Ap Gp Gp Ap (Ped)p Gp Ap Ap Gp Cp C)- 3'. Chain: i, j, k, l. Engineered: yes. Formamidopyrimidine-DNA glycosylase.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: fpg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dodecamer (from PQS)
Resolution:
2.10Å     R-factor:   0.214     R-free:   0.265
Authors: R.Gilboa,D.O.Zharkov,G.Golan,A.S.Fernandes,S.E.Gerchman, E.Matz,J.H.Kycia,A.P.Grollman,G.Shoham
Key ref:
R.Gilboa et al. (2002). Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem, 277, 19811-19816. PubMed id: 11912217 DOI: 10.1074/jbc.M202058200
Date:
22-Oct-01     Release date:   14-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05523  (FPG_ECOLI) -  Formamidopyrimidine-DNA glycosylase
Seq:
Struc:
269 a.a.
260 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.2.2.23  - DNA-formamidopyrimidine glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
   Enzyme class 3: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   8 terms 
  Biochemical function     catalytic activity     15 terms  

 

 
DOI no: 10.1074/jbc.M202058200 J Biol Chem 277:19811-19816 (2002)
PubMed id: 11912217  
 
 
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, G.Shoham.
 
  ABSTRACT  
 
Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. The Schiff base intermediate formed during this reaction between Escherichia coli Fpg and DNA was trapped by reduction with sodium borohydride, and the structure of the resulting covalently cross-linked complex was determined at a 2.1-A resolution. Fpg is a bilobal protein with a wide, positively charged DNA-binding groove. It possesses a conserved zinc finger and a helix-two turn-helix motif that participate in DNA binding. The absolutely conserved residues Lys-56, His-70, Asn-168, and Arg-258 form hydrogen bonds to the phosphodiester backbone of DNA, which is sharply kinked at the lesion site. Residues Met-73, Arg-109, and Phe-110 are inserted into the DNA helix, filling the void created by nucleotide eversion. A deep hydrophobic pocket in the active site is positioned to accommodate an everted base. Structural analysis of the Fpg-DNA complex reveals essential features of damage recognition and the catalytic mechanism of Fpg.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Schematic representation of Fpg-DNA interactions. The central nucleotides of the modified and complementary strands are 8-oxoG0 and C^(0), respectively. Nucleotides are numbered as shown with those in the complementary strand in parentheses.
Figure 6.
Fig. 6. Scheme of principal steps in the sequence of reactions catalyzed by Fpg, showing catalytically important amino acid residues. Nucleophilic attack at C1' and protonation at O4' (a) lead to base displacement and deoxyribose ring opening. A Schiff base involving Pro-1 is formed with O4' stabilized by hydrogen bonding to Glu-2. b, following abstraction of the 2' proton of deoxyribose by a general base, Lys-56 protonates the 3'-phosphate leading to -elimination (c). Deprotonation of C4', now vinilogous to C1', is followed by protonation of the 5'-phosphate by Arg-258 and the second -elimination event (c).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 19811-19816) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20175991 I.R.Grin, R.A.Rieger, and D.O.Zharkov (2010).
Inactivation of NEIL2 DNA glycosylase by pyridoxal phosphate reveals a loop important for substrate binding.
  Biochem Biophys Res Commun, 394, 100-105.  
20031487 Y.Guo, V.Bandaru, P.Jaruga, X.Zhao, C.J.Burrows, S.Iwai, M.Dizdaroglu, J.P.Bond, and S.S.Wallace (2010).
The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts.
  DNA Repair (Amst), 9, 177-190.  
19151100 H.Sanada, T.Nakanishi, H.Inoue, and M.Kitamura (2009).
Cloning and expression of the MutM gene from obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F).
  J Biochem, 145, 525-532.  
19916941 I.R.Grin, P.G.Konorovsky, G.A.Nevinsky, and D.O.Zharkov (2009).
Heavy metal ions affect the activity of DNA glycosylases of the fpg family.
  Biochemistry (Mosc), 74, 1253-1259.  
19625256 K.Imamura, S.S.Wallace, and S.Doublié (2009).
Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA.
  J Biol Chem, 284, 26174-26183.
PDB codes: 3a42 3a45 3a46
19134198 K.L.Tibballs, O.H.Ambur, K.Alfsnes, H.Homberset, S.A.Frye, T.Davidsen, and T.Tønjum (2009).
Characterization of the meningococcal DNA glycosylase Fpg involved in base excision repair.
  BMC Microbiol, 9, 7.  
19218779 N.Shikazono, M.Noguchi, K.Fujii, A.Urushibara, and A.Yokoya (2009).
The yield, processing, and biological consequences of clustered DNA damage induced by ionizing radiation.
  J Radiat Res (Tokyo), 50, 27-36.  
19217358 S.D.Kathe, R.Barrantes-Reynolds, P.Jaruga, M.R.Newton, C.J.Burrows, V.Bandaru, M.Dizdaroglu, J.P.Bond, and S.S.Wallace (2009).
Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases.
  DNA Repair (Amst), 8, 643-653.  
18369869 A.Görg, C.Lück, and W.Weiss (2008).
Sample prefractionation in granulated sephadex IEF gels.
  Methods Mol Biol, 424, 277-286.  
18682218 B.R.Bowman, S.Lee, S.Wang, and G.L.Verdine (2008).
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
  Structure, 16, 1166-1174.
PDB codes: 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu
18172202 C.A.Minetti, D.P.Remeta, and K.J.Breslauer (2008).
A continuous hyperchromicity assay to characterize the kinetics and thermodynamics of DNA lesion recognition and base excision.
  Proc Natl Acad Sci U S A, 105, 70-75.  
18506863 H.Mueller, M.Hopfinger, and T.Carell (2008).
Synthesis of a stabilized version of the imidazolone DNA lesion.
  Chembiochem, 9, 1617-1622.  
18166975 M.L.Hegde, T.K.Hazra, and S.Mitra (2008).
Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.
  Cell Res, 18, 27-47.  
18557781 V.S.Sidorenko, G.V.Mechetin, G.A.Nevinsky, and D.O.Zharkov (2008).
Ionic strength and magnesium affect the specificity of Escherichia coli and human 8-oxoguanine-DNA glycosylases.
  FEBS J, 275, 3747-3760.  
18457574 V.S.Sidorenko, M.A.Rot, M.L.Filipenko, G.A.Nevinsky, and D.O.Zharkov (2008).
Novel DNA glycosylases from Mycobacterium tuberculosis.
  Biochemistry (Mosc), 73, 442-450.  
17382378 G.Frosina (2007).
Gene prophylaxis by a DNA repair function.
  Mol Aspects Med, 28, 323-344.  
17289752 J.O.Blaisdell, and S.S.Wallace (2007).
Rapid determination of the active fraction of DNA repair glycosylases: a novel fluorescence assay for trapped intermediates.
  Nucleic Acids Res, 35, 1601-1611.  
17655276 N.Krishnamurthy, J.G.Muller, C.J.Burrows, and S.S.David (2007).
Unusual structural features of hydantoin lesions translate into efficient recognition by Escherichia coli Fpg.
  Biochemistry, 46, 9355-9365.  
17715144 S.Couvé-Privat, G.Macé, F.Rosselli, and M.K.Saparbaev (2007).
Psoralen-induced DNA adducts are substrates for the base excision repair pathway in human cells.
  Nucleic Acids Res, 35, 5672-5682.  
17627905 V.Bandaru, X.Zhao, M.R.Newton, C.J.Burrows, and S.S.Wallace (2007).
Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus.
  DNA Repair (Amst), 6, 1629-1641.  
16432839 G.Frosina (2006).
Prophylaxis of oxidative DNA damage by formamidopyrimidine-DNA glycosylase.
  Int J Cancer, 119, 1-7.  
16885468 G.W.Buchko, C.Y.Kim, T.C.Terwilliger, and M.A.Kennedy (2006).
Solution structure of the conserved hypothetical protein Rv2302 from Mycobacterium tuberculosis.
  J Bacteriol, 188, 5993-6001.
PDB code: 2a7y
17002303 K.Y.Kropachev, D.O.Zharkov, and A.P.Grollman (2006).
Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger.
  Biochemistry, 45, 12039-12049.  
17115714 R.K.Walker, A.K.McCullough, and R.S.Lloyd (2006).
Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.
  Biochemistry, 45, 14192-14200.  
16145054 G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.Kycia, A.P.Grollman, and G.Shoham (2005).
Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.
  Nucleic Acids Res, 33, 5006-5016.
PDB codes: 1q39 1q3b 1q3c
16129732 J.L.Parsons, D.O.Zharkov, and G.L.Dianov (2005).
NEIL1 excises 3' end proximal oxidative DNA lesions resistant to cleavage by NTH1 and OGG1.
  Nucleic Acids Res, 33, 4849-4856.  
16243784 K.Pereira de Jésus, L.Serre, C.Zelwer, and B.Castaing (2005).
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, 33, 5936-5944.
PDB codes: 1nnj 1pji 1pjj 1pm5
15103129 A.Teplitsky, A.Mechaly, V.Stojanoff, G.Sainz, G.Golan, H.Feinberg, R.Gilboa, V.Reiland, G.Zolotnitsky, D.Shallom, A.Thompson, Y.Shoham, and G.Shoham (2004).
Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 836-848.
PDB code: 1hiz
15272182 G.Golan, D.O.Zharkov, A.S.Fernandes, E.Zaika, J.H.Kycia, Z.Wawrzak, A.P.Grollman, and G.Shoham (2004).
Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed form.
  Acta Crystallogr D Biol Crystallogr, 60, 1476-1480.  
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
15175427 K.K.Bhakat, T.K.Hazra, and S.Mitra (2004).
Acetylation of the human DNA glycosylase NEIL2 and inhibition of its activity.
  Nucleic Acids Res, 32, 3033-3039.  
15273302 P.Amara, L.Serre, B.Castaing, and A.Thomas (2004).
Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics.
  Protein Sci, 13, 2009-2021.  
15232006 S.Doublié, V.Bandaru, J.P.Bond, and S.S.Wallace (2004).
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, 101, 10284-10289.
PDB code: 1tdh
14769949 V.V.Koval, N.A.Kuznetsov, D.O.Zharkov, A.A.Ishchenko, K.T.Douglas, G.A.Nevinsky, and O.S.Fedorova (2004).
Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase.
  Nucleic Acids Res, 32, 926-935.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
12840008 J.C.Fromme, and G.L.Verdine (2003).
Structure of a trapped endonuclease III-DNA covalent intermediate.
  EMBO J, 22, 3461-3471.
PDB codes: 1orn 1orp 1p59
12505993 K.D.Corbett, and J.M.Berger (2003).
Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution.
  EMBO J, 22, 151-163.
PDB codes: 1mu5 1mx0
12846827 M.Taranenko, A.Rykhlevskaya, M.Mtchedlidze, J.Laval, and S.Kuznetsova (2003).
Photochemical cross-linking of Escherichia coli Fpg protein to DNA duplexes containing phenyl(trifluoromethyl)diazirine groups.
  Eur J Biochem, 270, 2945-2949.  
12434002 H.Terato, A.Masaoka, K.Asagoshi, A.Honsho, Y.Ohyama, T.Suzuki, M.Yamada, K.Makino, K.Yamamoto, and H.Ide (2002).
Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid.
  Nucleic Acids Res, 30, 4975-4984.  
12433996 I.Morland, V.Rolseth, L.Luna, T.Rognes, M.Bjørås, and E.Seeberg (2002).
Human DNA glycosylases of the bacterial Fpg/MutM superfamily: an alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA.
  Nucleic Acids Res, 30, 4926-4936.  
12055620 J.C.Fromme, and G.L.Verdine (2002).
Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM.
  Nat Struct Biol, 9, 544-552.
PDB codes: 1l1t 1l1z 1l2b 1l2c 1l2d
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.