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PDBsum entry 1k3x

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protein dna_rna ligands metals links
Hydrolase/DNA PDB id
1k3x
Jmol
Contents
Protein chain
253 a.a. *
DNA/RNA
Ligands
SO4 ×5
GOL ×4
Metals
_ZN
Waters ×488
* Residue conservation analysis
PDB id:
1k3x
Name: Hydrolase/DNA
Title: Crystal structure of a trapped reaction intermediate of the enzyme endonuclease viii with brominated-DNA
Structure: 5'-d( Gp Gp Cp (Bru)p (Bru)p Cp Ap (Bru)p Cp Cp ( P Gp G)-3'. Chain: b. Engineered: yes. 5'-d( Cp Cp Ap Gp Gp Ap (Ped)p Gp Ap Ap Gp Cp C)- chain: c. Engineered: yes. Endonuclease viii. Chain: a.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: nei. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.25Å     R-factor:   0.149     R-free:   0.181
Authors: G.Golan,D.O.Zharkov,R.Gilboa,A.S.Fernandes,J.H.Kycia,S.E.Ger R.A.Rieger,A.P.Grollman,G.Shoham
Key ref:
D.O.Zharkov et al. (2002). Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. EMBO J, 21, 789-800. PubMed id: 11847126 DOI: 10.1093/emboj/21.4.789
Date:
04-Oct-01     Release date:   04-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P50465  (END8_ECOLI) -  Endonuclease 8
Seq:
Struc:
263 a.a.
253 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     13 terms  

 

 
DOI no: 10.1093/emboj/21.4.789 EMBO J 21:789-800 (2002)
PubMed id: 11847126  
 
 
Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
D.O.Zharkov, G.Golan, R.Gilboa, A.S.Fernandes, S.E.Gerchman, J.H.Kycia, R.A.Rieger, A.P.Grollman, G.Shoham.
 
  ABSTRACT  
 
Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. However, Nei differs significantly from Fpg in substrate specificity. We determined the structure of Nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 A resolution. The crosslink is derived from a Schiff base intermediate that precedes beta-elimination and is stabilized by reduction with NaBH(4). Nei consists of two domains connected by a hinge region, creating a DNA binding cleft between domains. DNA in the complex is sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted from the duplex into the active site. Amino acids involved in substrate binding and catalysis are identified. Molecular modeling and analysis of amino acid conservation suggest a site for recognition of the damaged base. Based on structural features of the complex and site-directed mutagenesis studies, we propose a catalytic mechanism for Nei.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Scheme of Nei−DNA interactions. Nucleotides are numbered beginning from Tg^0, positive towards the 5'-end, with superscript in parentheses for the complementary strand. Only the central 9 bp are shown. Hydrogen bonds are shown as arrows pointing towards their respective acceptors. Leu70, Tyr71 and Pro253 form van der Waals contacts with nearby DNA residues.
Figure 8.
Figure 8 Central region of the DNA duplex in the Nei−DNA complex. Protein residues that fill the void in DNA created by Tg eversion are shown as solid (cyan) spheres. DNA is presented as a ball-and-stick model with dotted van der Waals radii; dRbl in red, the remaining DNA in yellow.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 789-800) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220122 B.Dalhus, M.Forsbring, I.H.Helle, E.S.Vik, R.J.Forstrøm, P.H.Backe, I.Alseth, and M.Bjørås (2011).
Separation-of-function mutants unravel the dual-reaction mode of human 8-oxoguanine DNA glycosylase.
  Structure, 19, 117-127.
PDB code: 2xhi
21280021 H.E.Peckham, and W.K.Olson (2011).
Nucleic-acid structural deformability deduced from anisotropic displacement parameters.
  Biopolymers, 95, 254-269.  
20005182 I.D.Odell, K.Newick, N.H.Heintz, S.S.Wallace, and D.S.Pederson (2010).
Non-specific DNA binding interferes with the efficient excision of oxidative lesions from chromatin by the human DNA glycosylase, NEIL1.
  DNA Repair (Amst), 9, 134-143.  
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.  
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
19443904 M.Forsbring, E.S.Vik, B.Dalhus, T.H.Karlsen, A.Bergquist, E.Schrumpf, M.Bjørås, K.M.Boberg, and I.Alseth (2009).
Catalytically impaired hMYH and NEIL1 mutant proteins identified in patients with primary sclerosing cholangitis and cholangiocarcinoma.
  Carcinogenesis, 30, 1147-1154.  
19258314 S.Couvé, G.Macé-Aimé, F.Rosselli, and M.K.Saparbaev (2009).
The Human Oxidative DNA Glycosylase NEIL1 Excises Psoralen-induced Interstrand DNA Cross-links in a Three-stranded DNA Structure.
  J Biol Chem, 284, 11963-11970.  
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
18004751 J.W.Torrance, M.W.Macarthur, and J.M.Thornton (2008).
Evolution of binding sites for zinc and calcium ions playing structural roles.
  Proteins, 71, 813-830.  
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.  
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.  
17114185 C.T.Radom, A.Banerjee, and G.L.Verdine (2007).
Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.
  J Biol Chem, 282, 9182-9194.
PDB codes: 2nob 2noe 2nof 2noh 2noi 2nol 2noz
17485665 J.Mrázek, X.Guo, and A.Shah (2007).
Simple sequence repeats in prokaryotic genomes.
  Proc Natl Acad Sci U S A, 104, 8472-8477.  
17432829 L.Jia, V.Shafirovich, N.E.Geacintov, and S.Broyde (2007).
Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies.
  Biochemistry, 46, 5305-5314.  
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.  
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.  
15339932 A.Das, L.Rajagopalan, V.S.Mathura, S.J.Rigby, S.Mitra, and T.K.Hazra (2004).
Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein.
  J Biol Chem, 279, 47132-47138.
PDB code: 1vzp
14734554 A.Katafuchi, T.Nakano, A.Masaoka, H.Terato, S.Iwai, F.Hanaoka, and H.Ide (2004).
Differential specificity of human and Escherichia coli endonuclease III and VIII homologues for oxidative base lesions.
  J Biol Chem, 279, 14464-14471.  
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
14607836 E.I.Zaika, R.A.Perlow, E.Matz, S.Broyde, R.Gilboa, A.P.Grollman, and D.O.Zharkov (2004).
Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis.
  J Biol Chem, 279, 4849-4861.  
15249553 F.Coste, M.Ober, T.Carell, S.Boiteux, C.Zelwer, and B.Castaing (2004).
Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.
  J Biol Chem, 279, 44074-44083.
PDB codes: 1tdz 1xc8
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.  
14967139 J.C.Connelly, and D.R.Leach (2004).
Repair of DNA covalently linked to protein.
  Mol Cell, 13, 307-316.  
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
14661275 A.David, N.Bleimling, C.Beuck, J.M.Lehn, E.Weinhold, and M.P.Teulade-Fichou (2003).
DNA mismatch-specific base flipping by a bisacridine macrocycle.
  Chembiochem, 4, 1326-1331.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
14522990 H.Dou, S.Mitra, and T.K.Hazra (2003).
Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2.
  J Biol Chem, 278, 49679-49684.  
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
14525999 J.C.Fromme, and G.L.Verdine (2003).
DNA lesion recognition by the bacterial repair enzyme MutM.
  J Biol Chem, 278, 51543-51548.
PDB codes: 1r2y 1r2z
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
12719419 T.Nakano, H.Terato, K.Asagoshi, A.Masaoka, M.Mukuta, Y.Ohyama, T.Suzuki, K.Makino, and H.Ide (2003).
DNA-protein cross-link formation mediated by oxanine. A novel genotoxic mechanism of nitric oxide-induced DNA damage.
  J Biol Chem, 278, 25264-25272.  
12057763 D.O.Zharkov, and A.P.Grollman (2002).
Combining structural and bioinformatics methods for the analysis of functionally important residues in DNA glycosylases.
  Free Radic Biol Med, 32, 1254-1263.  
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
12065399 L.Serre, K.Pereira de Jésus, S.Boiteux, C.Zelwer, and B.Castaing (2002).
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
  EMBO J, 21, 2854-2865.
PDB codes: 1kfv 7abc
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 code is shown on the right.