PDBsum entry 4m9n

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
Protein chain
300 a.a.
_NA ×2
Waters ×234
PDB id:
Name: Transferase/DNA
Title: DNA polymerase beta e295k soaked with datp
Structure: DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. DNA template strand. Chain: t. Engineered: yes. DNA primer strand. Chain: p.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: DNA template strand, 16mer. Other_details: DNA primer strand, 10mer.
2.27Å     R-factor:   0.195     R-free:   0.227
Authors: B.E.Eckenroth,S.Doublie
Key ref: B.E.Eckenroth et al. (2013). The E295K cancer variant of human polymerase β favors the mismatch conformational pathway during nucleotide selection. J Biol Chem, 288, 34850-34860. PubMed id: 24133209 DOI: 10.1074/jbc.M113.510891
14-Aug-13     Release date:   16-Oct-13    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
335 a.a.
300 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.  - 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
+ 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   5 terms 
  Biological process     DNA biosynthetic process   12 terms 
  Biochemical function     protein binding     11 terms  


DOI no: 10.1074/jbc.M113.510891 J Biol Chem 288:34850-34860 (2013)
PubMed id: 24133209  
The E295K cancer variant of human polymerase β favors the mismatch conformational pathway during nucleotide selection.
B.E.Eckenroth, J.B.Towle-Weicksel, J.B.Sweasy, S.Doublié.
DNA polymerase β (pol β) is responsible for gap filling synthesis during repair of damaged DNA as part of the base excision repair pathway. Human pol β mutations were recently identified in a high percentage (∼30%) of tumors. Characterization of specific cancer variants is particularly useful to further the understanding of the general mechanism of pol β while providing context to disease contribution. We showed that expression of the carcinoma variant E295K induces cellular transformation. The poor polymerase activity exhibited by the variant was hypothesized to be caused by the destabilization of proper active site assembly by the glutamate to lysine mutation. Here, we show that this variant exhibits an unusual preference for binding dCTP opposite a templating adenine over the cognate dTTP. Biochemical studies indicate that the noncognate competes with the cognate nucleotide for binding to the polymerase active site with the noncognate incorporation a function of higher affinity and not increased activity. In the crystal structure of the variant bound to dA:dCTP, the fingers domain closes around the mismatched base pair. Nucleotide incorporation is hindered because key residues in the polymerase active site are not properly positioned for nucleotidyl transfer. In contrast to the noncognate dCTP, neither the cognate dTTP nor its nonhydrolyzable analog induced fingers closure, as isomorphous difference Fourier maps show that the cognate nucleotides are bound to the open state of the polymerase. Comparison with published structures provides insight into the structural rearrangements within pol β that occur during the process of nucleotide discrimination.