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PDBsum entry 4fbu

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protein dna_rna metals Protein-protein interface(s) links
Transferase/DNA PDB id
4fbu
Jmol
Contents
Protein chains
341 a.a.
DNA/RNA
Metals
_CA ×4
Waters ×248
PDB id:
4fbu
Name: Transferase/DNA
Title: Dpo4 polymerase pre-insertion binary complex with the n- (deoxyguanosin-8-yl)-1-aminopyrene lesion
Structure: DNA polymerase iv. Chain: a, b. Synonym: pol iv. Engineered: yes. DNA primer. Chain: p, d. Engineered: yes. DNA template. Chain: t, c.
Source: Sulfolobus solfataricus. Organism_taxid: 273057. Strain: atcc 35092 / dsm 1617 / jcm 11322 / p2. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA
Resolution:
2.60Å     R-factor:   0.220     R-free:   0.261
Authors: K.Kirouac,A.Basu,H.Ling
Key ref: K.N.Kirouac et al. (2013). Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase. J Mol Biol, 425, 4167-4176. PubMed id: 23876706 DOI: 10.1016/j.jmb.2013.07.020
Date:
23-May-12     Release date:   12-Jun-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q97W02  (DPO4_SULSO) -  DNA polymerase IV
Seq:
Struc:
352 a.a.
341 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
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     transferase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2013.07.020 J Mol Biol 425:4167-4176 (2013)
PubMed id: 23876706  
 
 
Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase.
K.N.Kirouac, A.K.Basu, H.Ling.
 
  ABSTRACT  
 
Polycyclic aromatic hydrocarbons and their nitro derivatives are culprits of the detrimental health effects of environmental pollution. These hydrophobic compounds metabolize to reactive species and attach to DNA producing bulky lesions, such as N-[deoxyguanosine-8-yl]-1-aminopyrene (APG), in genomic DNA. The bulky adducts block DNA replication by high-fidelity polymerases and compromise replication fidelities and efficiencies by specialized lesion bypass polymerases. Here we present three crystal structures of the DNA polymerase Dpo4, a model translesion DNA polymerase of the Y family, in complex with APG-lesion-containing DNA in pre-insertion and extension stages. APG is captured in two conformations in the pre-insertion complex; one is highly exposed to the solvent, whereas the other is harbored in a shallow cleft between the finger and unique Y family little finger domain. In contrast, APG is in a single conformation at the extension stage, in which the pyrene ring is sandwiched between the little finger domain and a base from the turning back single-stranded template strand. Strikingly, a nucleotide intercalates the DNA helix to form a quaternary complex with Dpo4, DNA, and an incoming nucleotide, which stabilizes the distorted DNA structure at the extension stage. The unique APG DNA conformations in Dpo4 inhibit DNA translocation through the polymerase active site for APG bypass. We also modeled an insertion complex that illustrates a solvent-exposed pyrene ring contributing to an unstable insertion state. The structural work combined with our lesion replication assays provides a novel structural mechanism on bypass of DNA adducts containing polycyclic aromatic hydrocarbon moieties.