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PDBsum entry 3epi

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
3epi
Jmol
Contents
Protein chain
373 a.a. *
DNA/RNA
Ligands
PO4
Metals
_NA
Waters ×69
* Residue conservation analysis
PDB id:
3epi
Name: Transferase/DNA
Title: Structure of human DNA polymerase iota complexed with n2-eth and incoming ttp
Structure: DNA polymerase iota. Chain: a. Fragment: catalytic fragment (unp residues 1-420). Synonym: rad30 homolog b, eta2. Engineered: yes. 5'-d( Dtp Dcp Dtp (2Eg) p Dgp Dgp Dgp Dtp Dcp Dcp Dtp Dap Dgp Dgp Dap Dcp Dcp (Doc) chain: b, c. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: poli, rad30b. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: a self-annealing oligonucletoide was synthes midland certified reagents containing n2-ethylgaunine using
Resolution:
2.90Å     R-factor:   0.239     R-free:   0.282
Authors: M.G.Pence
Key ref:
M.G.Pence et al. (2009). Lesion bypass of N2-ethylguanine by human DNA polymerase iota. J Biol Chem, 284, 1732-1740. PubMed id: 18984581 DOI: 10.1074/jbc.M807296200
Date:
29-Sep-08     Release date:   16-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota
Seq:
Struc:
 
Seq:
Struc:
740 a.a.
373 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
=
diphosphate
Bound ligand (Het Group name = PO4)
matches with 55.56% similarity
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   1 term 
  Biochemical function     damaged DNA binding     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M807296200 J Biol Chem 284:1732-1740 (2009)
PubMed id: 18984581  
 
 
Lesion bypass of N2-ethylguanine by human DNA polymerase iota.
M.G.Pence, P.Blans, C.N.Zink, T.Hollis, J.C.Fishbein, F.W.Perrino.
 
  ABSTRACT  
 
Nucleotide incorporation and extension opposite N2-ethyl-Gua by DNA polymerase iota was measured and structures of the DNA polymerase iota-N2-ethyl-Gua complex with incoming nucleotides were solved. Efficiency and fidelity of DNA polymerase iota opposite N2-ethyl-Gua was determined by steady state kinetic analysis with Mg2+ or Mn2+ as the activating metal. DNA polymerase iota incorporates dCMP opposite N2-ethyl-Gua and unadducted Gua with similar efficiencies in the presence of Mg2+ and with greater efficiencies in the presence of Mn2+. However, the fidelity of nucleotide incorporation by DNA polymerase iota opposite N2-ethyl-Gua and Gua using Mn2+ is lower relative to that using Mg2+ indicating a metal-dependent effect. DNA polymerase iota extends from the N2-ethyl-Gua:Cyt 3' terminus more efficiently than from the Gua:Cyt base pair. Together these kinetic data indicate that the DNA polymerase iota catalyzed reaction is well suited for N(2)-ethyl-Gua bypass. The structure of DNA polymerase iota with N2-ethyl-Gua at the active site reveals the adducted base in the syn configuration when the correct incoming nucleotide is present. Positioning of the ethyl adduct into the major groove removes potential steric overlap between the adducted template base and the incoming dCTP. Comparing structures of DNA polymerase iota complexed with N2-ethyl-Gua and Gua at the active site suggests movements in the DNA polymerase iota polymerase-associated domain to accommodate the adduct providing direct evidence that DNA polymerase iota efficiently replicates past a minor groove DNA adduct by positioning the adducted base in the syn configuration.
 
  Selected figure(s)  
 
Figure 2.
The structures of DNA pol ι·N^2-ethyl-Gua Complexes with incoming dCTP or dTTP. A, the structure of DNA pol ι containing N^2-ethyl-Gua and incoming dCTP shows the N^2-ethyl-Gua base rotated into the syn configuration. B, the structure of DNA pol ι containing N^2-ethyl-Gua and incoming dTTP shows the N^2-ethyl-Gua base in the anti configuration and the N^2-adduct protruding into the minor groove. C, electron density around the N^2-ethyl adduct and incoming dCTP. D, electron density around the N^2-ethyl adduct and the γ phosphate of the incoming dTTP.
Figure 4.
Repositioning of Lys^309 in the structure of DNA pol ι with N^2-ethyl-Gua in the syn configuration. A, the Lys^309 side chain in DNA pol ι in complex with N^2-ethyl-Gua (green) in the syn configuration shifts ∼9Å relative to the position of Lys^309 in DNA pol ι complexed with syn Gua (PDB code 2ALZ, magenta). B, with N^2-ethyl-Gua in the anti conformation (blue) Lys^309 remains in a similar position relative to the Lys^309 in the DNA pol ι·Gua complex (PDB code 2FLP, yellow).
 
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2009, 284, 1732-1740) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
19616647 M.T.Washington, K.D.Carlson, B.D.Freudenthal, and J.M.Pryor (2010).
Variations on a theme: eukaryotic Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1113-1123.  
19367366 C.Guo, J.N.Kosarek-Stancel, T.S.Tang, and E.C.Friedberg (2009).
Y-family DNA polymerases in mammalian cells.
  Cell Mol Life Sci, 66, 2363-2381.  
19542237 H.Zhang, R.L.Eoff, I.D.Kozekov, C.J.Rizzo, M.Egli, and F.P.Guengerich (2009).
Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes.
  J Biol Chem, 284, 17687-17699.
PDB codes: 2w9a 2w9b 2w9c
19397281 I.G.Minko, I.D.Kozekov, T.M.Harris, C.J.Rizzo, R.S.Lloyd, and M.P.Stone (2009).
Chemistry and biology of DNA containing 1,N(2)-deoxyguanosine adducts of the alpha,beta-unsaturated aldehydes acrolein, crotonaldehyde, and 4-hydroxynonenal.
  Chem Res Toxicol, 22, 759-778.  
19767609 K.Donny-Clark, and S.Broyde (2009).
Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion.
  Nucleic Acids Res, 37, 7095-7109.  
19440206 K.N.Kirouac, and H.Ling (2009).
Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota.
  EMBO J, 28, 1644-1654.
PDB codes: 3gv5 3gv7 3gv8
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.