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PDBsum entry 4kls

Go to PDB code: 
protein dna_rna ligands metals links
Transferase, lyase/DNA PDB id
4kls
Jmol PyMol
Contents
Protein chain
324 a.a.
DNA/RNA
Ligands
DTP
PPV
Metals
_NA ×3
_MN ×3
Waters ×213
PDB id:
4kls
Name: Transferase, lyase/DNA
Title: DNA polymerase beta mismatched reactant complex with mn2+, 1
Structure: DNA polymerase beta. Chain: a. Engineered: yes. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp Cp A)-3'. Chain: p. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
1.98Å     R-factor:   0.229     R-free:   0.285
Authors: B.D.Freudenthal,W.A.Beard,D.D.Shock,S.H.Wilson
Key ref: B.D.Freudenthal et al. (2013). Observing a DNA polymerase choose right from wrong. Cell, 154, 157-168. PubMed id: 23827680 DOI: 10.1016/j.cell.2013.05.048
Date:
07-May-13     Release date:   17-Jul-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
Seq:
Struc:
335 a.a.
324 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
Bound ligand (Het Group name = DTP)
matches with 64.52% similarity
+ DNA(n)
=
diphosphate
Bound ligand (Het Group name = PPV)
corresponds exactly
+ 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.cell.2013.05.048 Cell 154:157-168 (2013)
PubMed id: 23827680  
 
 
Observing a DNA polymerase choose right from wrong.
B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson.
 
  ABSTRACT  
 
DNA polymerase (pol) β is a model polymerase involved in gap-filling DNA synthesis utilizing two metals to facilitate nucleotidyl transfer. Previous structural studies have trapped catalytic intermediates by utilizing substrate analogs (dideoxy-terminated primer or nonhydrolysable incoming nucleotide). To identify additional intermediates during catalysis, we now employ natural substrates (correct and incorrect nucleotides) and follow product formation in real time with 15 different crystal structures. We are able to observe molecular adjustments at the active site that hasten correct nucleotide insertion and deter incorrect insertion not appreciated previously. A third metal binding site is transiently formed during correct, but not incorrect, nucleotide insertion. Additionally, long incubations indicate that pyrophosphate more easily dissociates after incorrect, compared to correct, nucleotide insertion. This appears to be coupled to subdomain repositioning that is required for catalytic activation/deactivation. The structures provide insights into a fundamental chemical reaction that impacts polymerase fidelity and genome stability.
 

 

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