PDBsum entry 3jpo

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protein dna_rna ligands metals links
Transferase/DNA PDB id
Jmol PyMol
Protein chain
326 a.a. *
_CL ×3
_NA ×3
Waters ×413
* Residue conservation analysis
PDB id:
Name: Transferase/DNA
Title: Ternary complex of DNA polymerase beta with a dideoxy termin primer and 2'-deoxyguanosine 5'-beta, gamma-monochloromethy triphosphate
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 (Doc))-3'. Chain: p. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic oligonucleotide. Other_details: synthetic oligonucleotide
2.00Å     R-factor:   0.194     R-free:   0.247
Authors: V.K.Batra,J.Upton,B.Kashmerov,W.A.Beard,S.H.Wilson,M.F.Goodm C.E.Mckenna
Key ref: V.K.Batra et al. (2010). Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. J Am Chem Soc, 132, 7617-7625. PubMed id: 20465217 DOI: 10.1021/ja909370k
04-Sep-09     Release date:   02-Jun-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
335 a.a.
326 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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
+ 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  


DOI no: 10.1021/ja909370k J Am Chem Soc 132:7617-7625 (2010)
PubMed id: 20465217  
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues.
V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.McKenna.
Beta,gamma-fluoromethylene analogues of nucleotides are considered to be useful mimics of the natural substrates, but direct structural evidence defining their active site interactions has not been available, including the influence of the new chiral center introduced at the CHF carbon, as in beta,gamma-fluoromethylene-dGTP, which forms an active site complex with DNA polymerase beta, a repair enzyme that plays an important role in base excision repair (BER) and oncogenesis. We report X-ray crystallographic results for a series of beta,gamma-CXY dGTP analogues, where X,Y = H, F, Cl, Br, and/or CH(3). For all three R/S monofluorinated analogues examined (CHF, 3/4; CCH(3)F, 13/14; CClF 15/16), a single CXF-diastereomer (3, 13, 16) is observed in the active site complex, with the CXF fluorine atom at a approximately 3 A (bonding) distance to a guanidinium N of Arg183. In contrast, for the CHCl, CHBr, and CHCH(3) analogues, both diasteromers (6/7, 8/9, 10/11) populate the dGTP site in the enzyme complex about equally. The structures of the bound dichloro (5) and dimethyl (12) analogue complexes indicate little to no steric effect on the placement of the bound nucleotide backbone. The results suggest that introduction of a single fluorine atom at the beta,gamma-bridging carbon atom of these dNTP analogues enables a new, stereospecific interaction within the preorganized active site complex that is unique to fluorine. The results also provide the first diverse structural data set permitting an assessment of how closely this class of dNTP analogues mimics the conformation of the parent nucleotide within the active site complex.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21117131 C.Dalvit, and A.Vulpetti (2011).
Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design.
  ChemMedChem, 6, 104-114.  
20724659 G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.McKenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, and G.A.Olah (2010).
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.
  Proc Natl Acad Sci U S A, 107, 15693-15698.
PDB code: 3lk9
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