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PDBsum entry 4f5p

Go to PDB code: 
protein dna_rna ligands metals links
Transferase, lyase/DNA PDB id
4f5p
Jmol PyMol
Contents
Protein chain
326 a.a.
DNA/RNA
Ligands
F2A
Metals
_MG
_NA ×2
Waters ×292
PDB id:
4f5p
Name: Transferase, lyase/DNA
Title: Open ternary mismatch complex of r283k DNA polymerase beta w analog
Structure: DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. DNA (5'-d( Cp Cp Gp Ap Cp Gp Gp Cp Gp Cp Ap Tp Cp 3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp C)-3').
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.
Resolution:
1.85Å     R-factor:   0.207     R-free:   0.245
Authors: B.D.Freudenthal,W.A.Beard,S.H.Wilson
Key ref: B.D.Freudenthal et al. (2012). Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure, 20, 1829-1837. PubMed id: 22959623 DOI: 10.1016/j.str.2012.08.008
Date:
13-May-12     Release date:   12-Dec-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
Seq:
Struc:
335 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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     protein complex   6 terms 
  Biological process     immunoglobulin heavy chain V-D-J recombination   27 terms 
  Biochemical function     protein binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2012.08.008 Structure 20:1829-1837 (2012)
PubMed id: 22959623  
 
 
Structures of dNTP intermediate states during DNA polymerase active site assembly.
B.D.Freudenthal, W.A.Beard, S.H.Wilson.
 
  ABSTRACT  
 
DNA polymerase and substrate conformational changes are essential for high-fidelity DNA synthesis. Structures of DNA polymerase (pol) β in complex with DNA show the enzyme in an "open" conformation. Subsequent to binding the nucleotide, the polymerase "closes" around the nascent base pair with two metals positioned for chemistry. However, structures of substrate/active site intermediates prior to closure are lacking. By destabilizing the closed complex, we determined unique ternary complex structures of pol β with correct and incorrect incoming nucleotides bound to the open conformation. These structures reveal that Watson-Crick hydrogen bonding is assessed upon initial complex formation. Importantly, nucleotide-bound states representing intermediate metal coordination states occur with active site assembly. The correct, but not incorrect, nucleotide maintains Watson-Crick hydrogen bonds during interconversion of these states. These structures indicate that the triphosphate of the incoming nucleotide undergoes rearrangement prior to closure, providing an opportunity to deter misinsertion and increase fidelity.
 

 

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