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PDBsum entry 2pxi

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protein dna_rna ligands metals links
Lyase, transferase/DNA PDB id
2pxi
Jmol PyMol
Contents
Protein chain
326 a.a. *
DNA/RNA
Ligands
GFH
Metals
_MG
_NA ×3
_CL ×5
Waters ×321
* Residue conservation analysis
PDB id:
2pxi
Name: Lyase, transferase/DNA
Title: Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma- monofluoromethylene triphosphate
Structure: DNA polymerase beta. Chain: a. Engineered: yes. 5'- d( Cp Cp Gp Ap Cp Cp Gp Cp Gp Cp Ap Tp Cp Ap Gp C)-3'. Chain: t. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp (Doc))-3'. Chain: p.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
2.10Å     R-factor:   0.206     R-free:   0.270
Authors: C.E.Mckenna,V.K.Batra,W.A.Beard,L.C.Pedersen,S.H.Wilson
Key ref: C.E.McKenna et al. (2007). (R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. J Am Chem Soc, 129, 15412-15413. PubMed id: 18031037
Date:
14-May-07     Release date:   08-Jan-08    
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

 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  

 

 
J Am Chem Soc 129:15412-15413 (2007)
PubMed id: 18031037  
 
 
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta.
C.E.McKenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, S.H.Wilson.
 
  ABSTRACT  
 
No abstract given.

 

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
19850352 E.Gaidamauskas, H.Parker, B.A.Kashemirov, A.A.Holder, K.Saejueng, C.E.McKenna, and D.C.Crans (2009).
Complexation of bisphosphonates with ytterbium(III): application of phosphate and ATP detection assay based on Yb(3+)-pyrocatechol violet.
  J Inorg Biochem, 103, 1652-1657.  
19391628 S.C.Kamerlin, C.E.McKenna, M.F.Goodman, M.F.Goondman, and A.Warshel (2009).
A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.
  Biochemistry, 48, 5963-5971.  
18811136 F.Liang, N.Jain, T.Hutchens, D.D.Shock, W.A.Beard, S.H.Wilson, M.P.Chiarelli, and B.P.Cho (2008).
Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides, 3,5'-cyclo-dG, and 2,5'-cyclo-dT.
  J Med Chem, 51, 6460-6470.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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