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protein dna_rna ligands metals links
Hydrolase/DNA PDB id
1orn
Jmol
Contents
Protein chain
214 a.a. *
DNA/RNA
Ligands
TRS
SF4
Metals
_NA
Waters ×105
* Residue conservation analysis
PDB id:
1orn
Name: Hydrolase/DNA
Title: Structure of a trapped endonuclease iii-DNA covalent intermediate: estranged-guanine complex
Structure: 5'-d( Ap Ap Gp Ap Cp Gp Tp Gp Gp Ap C)-3'. Chain: b. Engineered: yes. 5'-d( T Gp Tp Cp Cp Ap (Ped)p Gp Tp Cp T)-3'. Chain: c. Engineered: yes. Endonuclease iii. Chain: a. Engineered: yes
Source: Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: nth. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.70Å     R-factor:   0.235     R-free:   0.248
Authors: J.C.Fromme,G.L.Verdine
Key ref: J.C.Fromme and G.L.Verdine (2003). Structure of a trapped endonuclease III-DNA covalent intermediate. Embo J, 22, 3461-3471. PubMed id: 12840008 DOI: 10.1093/emboj/cdg311
Date:
14-Mar-03     Release date:   15-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

 

 
DOI no: 10.1093/emboj/cdg311 Embo J 22:3461-3471 (2003)
PubMed id: 12840008  
 
 
Structure of a trapped endonuclease III-DNA covalent intermediate.
J.C.Fromme, G.L.Verdine.
 
  ABSTRACT  
 
Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.
 

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
21036872 M.I.Ponferrada-Marín, J.T.Parrilla-Doblas, T.Roldán-Arjona, and R.R.Ariza (2011).
A discontinuous DNA glycosylase domain in a family of enzymes that excise 5-methylcytosine.
  Nucleic Acids Res, 39, 1473-1484.  
20047321 J.C.Genereux, A.K.Boal, and J.K.Barton (2010).
DNA-mediated charge transport in redox sensing and signaling.
  J Am Chem Soc, 132, 891-905.  
20110254 N.Matsumoto, T.Toga, R.Hayashi, K.Sugasawa, K.Katayanagi, H.Ide, I.Kuraoka, and S.Iwai (2010).
Fluorescent probes for the analysis of DNA strand scission in base excision repair.
  Nucleic Acids Res, 38, e101.  
19720997 A.K.Boal, J.C.Genereux, P.A.Sontz, J.A.Gralnick, D.K.Newman, and J.K.Barton (2009).
Redox signaling between DNA repair proteins for efficient lesion detection.
  Proc Natl Acad Sci U S A, 106, 15237-15242.  
19446526 F.Faucher, S.Duclos, V.Bandaru, S.S.Wallace, and S.Doublié (2009).
Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction.
  Structure, 17, 703-712.  
19361427 F.Faucher, S.M.Robey-Bond, S.S.Wallace, and S.Doublié (2009).
Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine.
  J Mol Biol, 387, 669-679.
PDB codes: 3f0z 3f10
19021503 F.W.Outten, and E.C.Theil (2009).
Iron-based redox switches in biology.
  Antioxid Redox Signal, 11, 1029-1046.  
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.  
18316718 A.A.Gorodetsky, L.E.Dietrich, P.E.Lee, B.Demple, D.K.Newman, and J.K.Barton (2008).
DNA binding shifts the redox potential of the transcription factor SoxR.
  Proc Natl Acad Sci U S A, 105, 3684-3689.  
18980370 A.A.Gorodetsky, M.C.Buzzeo, and J.K.Barton (2008).
DNA-mediated electrochemistry.
  Bioconjug Chem, 19, 2285-2296.  
18072751 J.C.Delaney, and J.M.Essigmann (2008).
Biological properties of single chemical-DNA adducts: a twenty year perspective.
  Chem Res Toxicol, 21, 232-252.  
17410210 A.H.Metz, T.Hollis, and B.F.Eichman (2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
  EMBO J, 26, 2411-2420.
PDB codes: 2ofi 2ofk
17599416 A.K.Boal, E.Yavin, and J.K.Barton (2007).
DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?
  J Inorg Biochem, 101, 1913-1921.  
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
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.  
17855402 X.Guan, A.Madabushi, D.Y.Chang, M.E.Fitzgerald, G.Shi, A.C.Drohat, and A.L.Lu (2007).
The human checkpoint sensor Rad9-Rad1-Hus1 interacts with and stimulates DNA repair enzyme TDG glycosylase.
  Nucleic Acids Res, 35, 6207-6218.  
16505354 E.Yavin, E.D.Stemp, V.L.O'shea, S.S.David, and J.K.Barton (2006).
Electron trap for DNA-bound repair enzymes: a strategy for DNA-mediated signaling.
  Proc Natl Acad Sci U S A, 103, 3610-3614.  
16547199 Y.Doi, A.Katafuchi, Y.Fujiwara, K.Hitomi, J.A.Tainer, H.Ide, and S.Iwai (2006).
Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction.
  Nucleic Acids Res, 34, 1540-1551.  
16155580 C.M.Bradley, D.R.Ronning, R.Ghirlando, R.Craigie, and F.Dyda (2005).
Structural basis for DNA bridging by barrier-to-autointegration factor.
  Nat Struct Mol Biol, 12, 935-936.
PDB code: 2bzf
15642264 G.M.Lingaraju, A.A.Sartori, D.Kostrewa, A.E.Prota, J.Jiricny, and F.K.Winkler (2005).
A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
  Structure, 13, 87-98.
PDB codes: 1xqo 1xqp
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.  
  15819980 K.A.Eriksen (2005).
Location of DNA damage by charge exchanging repair enzymes: effects of cooperativity on location time.
  Theor Biol Med Model, 2, 15.  
15606310 M.E.Lomax, H.Salje, S.Cunniffe, and P.O'Neill (2005).
8-OxoA inhibits the incision of an AP site by the DNA glycosylases Fpg, Nth and the AP endonuclease HAP1.
  Radiat Res, 163, 79-84.  
15811798 O.A.Lukianova, and S.S.David (2005).
A role for iron-sulfur clusters in DNA repair.
  Curr Opin Chem Biol, 9, 145-151.  
15615709 P.Jakimowicz, M.R.Cheesman, W.R.Bishai, K.F.Chater, A.J.Thomson, and M.J.Buttner (2005).
Evidence that the Streptomyces developmental protein WhiD, a member of the WhiB family, binds a [4Fe-4S] cluster.
  J Biol Chem, 280, 8309-8315.  
15766524 T.T.Lee, S.Agarwalla, and R.M.Stroud (2005).
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
  Cell, 120, 599-611.
PDB code: 2bh2
16096281 T.Watanabe, J.O.Blaisdell, S.S.Wallace, and J.P.Bond (2005).
Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses.
  J Biol Chem, 280, 34378-34384.  
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.  
15456766 C.Y.Lee, H.Bai, R.Houle, G.M.Wilson, and A.L.Lu (2004).
An Escherichia coli MutY mutant without the six-helix barrel domain is a dimer in solution and assembles cooperatively into multisubunit complexes with DNA.
  J Biol Chem, 279, 52653-52663.  
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.  
14961129 J.C.Fromme, A.Banerjee, S.J.Huang, and G.L.Verdine (2004).
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.
  Nature, 427, 652-656.
PDB codes: 1rrq 1rrs 1rrt 1vrl
14559969 E.M.Boon, A.L.Livingston, N.H.Chmiel, S.S.David, and J.K.Barton (2003).
DNA-mediated charge transport for DNA repair.
  Proc Natl Acad Sci U S A, 100, 12543-12547.  
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.