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PDBsum entry 2nq9
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protein dna_rna metals links
Hydrolase/DNA PDB id
2nq9

 

 

 

 

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Contents
Protein chain
279 a.a. *
DNA/RNA
Metals
_ZN ×3
Waters ×346
* Residue conservation analysis
PDB id:
2nq9
Name: Hydrolase/DNA
Title: High resolution crystal structure of escherichia coli endonuclease iv (endo iv) y72a mutant bound to damaged DNA
Structure: 5'-d( Ap Tp Ap Tp Cp T)-3'. Chain: b. Engineered: yes. 5'-d(p (3Dr)p Ap Gp Ap T)-3'. Chain: c. Engineered: yes. 5'-d( Ap Tp Cp Tp Gp Ap Ap Gp Tp Ap T)-3'. Chain: d. Engineered: yes.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: nfo. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.45Å     R-factor:   0.220     R-free:   0.234
Authors: E.D.Garcin-Hosfield,D.J.Hosfield,J.A.Tainer
Key ref:
E.D.Garcin et al. (2008). DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol, 15, 515-522. PubMed id: 18408731 DOI: 10.1038/nsmb.1414
Date:
30-Oct-06     Release date:   13-Nov-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A6C1  (END4_ECOLI) -  Endonuclease 4 from Escherichia coli (strain K12)
Seq:
Struc: 		285 a.a.
279 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  A-T-A-T-C-T 6 bases
  3DR-A-G-A-T 5 bases
  A-T-C-T-G-A-A-G-T-A-T 11 bases

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.2  - deoxyribonuclease Iv.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.

 

 
DOI no: 10.1038/nsmb.1414 Nat Struct Mol Biol 15:515-522 (2008)
PubMed id: 18408731  
 
 
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
E.D.Garcin, D.J.Hosfield, S.A.Desai, B.J.Haas, M.Björas, R.P.Cunningham, J.A.Tainer.
 
  ABSTRACT  
 
Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn3-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-A resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn2+ ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.
 
  Selected figure(s)  
 
Figure 2.
(a) Stereoview of DNA-free structure with coordination of the active-site phosphate and three Zn^2+ ions. Omit map is contoured at 2 (light blue) and 4 (dark blue) for the bound phosphate group. (b) AP DNA complex stereoview showing the three–metal ion active site (green spheres), residues Arg37, Tyr72 and Gln261 (pink), and bound DNA substrate with both the AP-site sugar and phosphate moieties and the cognate nucleotide (orange) flipped out from the DNA base stack. The 2F[o] - F[c] electron density map is contoured at 1 (blue mesh). (c) Stereoview of DNA substrate complex binding to active-site metal ions. Omit map (contoured at 2 , pink mesh) shows the intact phosphodiester bond (black arrow) that constrains the Zn[3] to Cyt6 O[3]' distance to 2.7 Å. 		Figure 3.
The structure of the Y72A mutant reveals cleaved AP DNA (a) and ordered water molecules (b) adjacent to the cleaved AP site (3 light blue and 4 dark blue contoured omit maps). Panels a and b are drawn in stereoview. (c) The structures of wild-type (left) and Y72A mutant (right) Endo IV bound to AP DNA product are virtually superimposable. Removal of the Tyr72 side chain allows increased solvation of the active site.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2008, 15, 515-522) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23396808 S.Classen, G.L.Hura, J.M.Holton, R.P.Rambo, I.Rodic, P.J.McGuire, K.Dyer, M.Hammel, G.Meigs, K.A.Frankel, and J.A.Tainer (2013).
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.
  J Appl Crystallogr, 46, 1.  
21353648 D.O.Onyango, A.Naguleswaran, S.Delaplane, A.Reed, M.R.Kelley, M.M.Georgiadis, and W.J.Sullivan (2011).
Base excision repair apurinic/apyrimidinic endonucleases in apicomplexan parasite Toxoplasma gondii.
  DNA Repair (Amst), 10, 466-475.  
21496641 S.E.Tsutakawa, S.Classen, B.R.Chapados, A.S.Arvai, L.D.Finger, G.Guenther, C.G.Tomlinson, P.Thompson, A.H.Sarker, B.Shen, P.K.Cooper, J.A.Grasby, and J.A.Tainer (2011).
Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily.
  Cell, 145, 198-211.
PDB codes: 3q8k 3q8l 3q8m
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20974932 B.Baños, L.Villar, M.Salas, and M.de Vega (2010).
Intrinsic apurinic/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites.
  Proc Natl Acad Sci U S A, 107, 19219-19224.  
20502938 J.L.Tubbs, and J.A.Tainer (2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
  Cell Mol Life Sci, 67, 3749-3762.  
20097063 R.P.Rambo, and J.A.Tainer (2010).
Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering.
  Curr Opin Struct Biol, 20, 128-137.  
19089001 C.Liu, and L.Wang (2009).
DNA hydrolytic cleavage catalyzed by synthetic multinuclear metallonucleases.
  Dalton Trans, (), 227-239.  
19516334 J.L.Tubbs, V.Latypov, S.Kanugula, A.Butt, M.Melikishvili, R.Kraehenbuehl, O.Fleck, A.Marriott, A.J.Watson, B.Verbeek, G.McGown, M.Thorncroft, M.F.Santibanez-Koref, C.Millington, A.S.Arvai, M.D.Kroeger, L.A.Peterson, D.M.Williams, M.G.Fried, G.P.Margison, A.E.Pegg, and J.A.Tainer (2009).
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
  Nature, 459, 808-813.
PDB codes: 3gva 3gx4 3gyh
19671525 N.K.Bernstein, M.Hammel, R.S.Mani, M.Weinfeld, M.Pelikan, J.A.Tainer, and J.N.Glover (2009).
Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase.
  Nucleic Acids Res, 37, 6161-6173.  
19734344 S.Kiyonari, S.Tahara, T.Shirai, S.Iwai, S.Ishino, and Y.Ishino (2009).
Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus.
  Nucleic Acids Res, 37, 6439-6453.  
18697748 K.Syson, C.Tomlinson, B.R.Chapados, J.R.Sayers, J.A.Tainer, N.H.Williams, and J.A.Grasby (2008).
Three metal ions participate in the reaction catalyzed by t5 flap endonuclease.
  J Biol Chem, 283, 28741-28746.  
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.

 

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