PDBsum entry 3c2m

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protein dna_rna ligands metals links
Transferase, lyase/DNA PDB id
Protein chain
326 a.a. *
EDO ×2
_NA ×6
_MN ×7
Waters ×307
* Residue conservation analysis
PDB id:
Name: Transferase, lyase/DNA
Title: Ternary complex of DNA polymerase beta with a g:dapcpp mismatch in the active site
Structure: DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'- d( Dcp Dcp Dgp Dap Dcp Dgp Dgp Dcp Dgp Dcp Dap Dtp Dcp Dap Dgp Dc)-3'). Chain: t. Engineered: yes. DNA (5'-
Source: Homo sapiens. Human. Gene: polb. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes
2.15Å     R-factor:   0.214     R-free:   0.270
Authors: V.K.Batra,W.A.Beard,D.D.Shock,L.C.Pedersen,S.H.Wilson
Key ref:
V.K.Batra et al. (2008). Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Mol Cell, 30, 315-324. PubMed id: 18471977 DOI: 10.1016/j.molcel.2008.02.025
25-Jan-08     Release date:   20-May-08    
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     cytoplasm   5 terms 
  Biological process     DNA biosynthetic process   12 terms 
  Biochemical function     protein binding     11 terms  


DOI no: 10.1016/j.molcel.2008.02.025 Mol Cell 30:315-324 (2008)
PubMed id: 18471977  
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson.
We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substituting Mn(2+) for Mg(2+) significantly decreases the fidelity of DNA synthesis. The structures reveal that the enzyme is in a closed conformation like that observed with a matched Watson-Crick base pair. The incorrect dAMPCPP binds in a conformation identical to that observed with the correct nucleotide. To accommodate the incorrect nucleotide and closed protein conformation, the template strand in the vicinity of the active site has shifted upstream over 3 A, removing the coding base from the active site and generating an abasic templating pocket. The primer terminus rotates as its complementary template base is repositioned. This rotation moves O3' of the primer terminus away from the alpha-phosphate of the incoming nucleotide, thereby deterring misincorporation.
  Selected figure(s)  
Figure 1.
Figure 1. Closed Conformation of the Ternary Substrate Complex with an Active-Site Mismatched Nascent Base Pair
(A) Licorice representation of the Pol β backbone of the binary DNA complex (PDB ID 1BPX; orange) and ternary substrate complex (green) with an incorrect incoming nucleotide (dAMPCPP; yellow carbons) with a templating guanine. The catalytic and DNA-binding subdomains superimposed (gray backbone) with an rmsd of 0.56 Å (177 Cα). The DNA is omitted for clarity, but the 5′→3′ direction of the primer entry into the active site is indicated with a solid arrow. The open and closed positions of α helix N are shown. The amino-terminal lyase domain and carboxyl-terminal N subdomain (colored) move in response to binding an incorrect dNTP. The amino- (N) and carboxyl-terminal (C) ends are labeled.
(B) Ribbon representation of the Pol β backbone of the ternary substrate complex with correct (gray) or incorrect (green) incoming nucleotides. The polymerase domains with a correct (dA-dUMPNPP; PDB ID 2FMS) and incorrect (dG-dAMPCPP) nascent base pair were superimposed with an rmsd of 0.62 Å (314 Cα). The superimposed structures indicate that α helix N is in a “closed” position like that observed with a Watson-Crick nascent base pair. The incoming dAMPCPP of the mismatch structure is shown (yellow carbons), but the DNA is omitted for clarity. The amino terminus (N) of the lyase domain is also indicated.
Figure 4.
Figure 4. Position of Key Protein Residues in Closed Polymerase Complexes with Correct or Incorrect Incoming Nucleotides
(A) Two views (major groove view, top; −90° rotation of the top view, bottom) of the nascent base pair of the mismatch structure (dG-dAMPCPP; green carbons) superimposed (see Figure 1) with that for a correctly matched base pair (gray carbons). The templating base is omitted from the correctly matched overlay for clarity. The structure illustrates the position of key protein side chains that can influence catalytic behavior. For catalytic activation with the correct incoming nucleotide, N subdomain closing is associated with the loss of a salt bridge between Arg258 (R258) and Asp192 (D192), which coordinate both active-site metals (M^2+), and the formation of hydrogen bonds (black dashed lines) with Glu295 (E295) and Tyr296 (Y296). Phe272 (F272) is repositioned in the closed complex to insulate Asp192 from Arg258. Arg283 (R283) that is situated in the N subdomain interacts with the minor groove edge of the templating strand (not shown). With an incorrect incoming nucleotide, R258 and R283 are in conformations that preclude catalytic activation. Arg283 is observed to hydrogen bond with the minor groove edge and phosphate backbone of the templating base. Other key residues (Asp192, Asn279, and Phe272) are observed in similar positions as that found with a correct incoming nucleotide.
(B) Major groove view of the nascent base pair of the dG/dC-dAMPCPP superimposed mismatch structures (dC template, light blue carbons; dG template, green carbons).
  The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2008, 30, 315-324) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21233421 K.Bebenek, L.C.Pedersen, and T.A.Kunkel (2011).
Replication infidelity via a mismatch with Watson-Crick geometry.
  Proc Natl Acad Sci U S A, 108, 1862-1867.
PDB codes: 3pml 3pmn 3pnc
21377475 P.Xie (2011).
A model for the dynamics of mammalian family X DNA polymerases.
  J Theor Biol, 277, 111-122.  
20673215 A.A.Kazakov, E.E.Grishina, V.Z.Tarantul, and L.V.Gening (2010).
Effect of human cell malignancy on activity of DNA polymerase iota.
  Biochemistry (Mosc), 75, 905-911.  
19631767 J.Yamtich, and J.B.Sweasy (2010).
DNA polymerase family X: function, structure, and cellular roles.
  Biochim Biophys Acta, 1804, 1136-1150.  
  19842163 R.Rucker, P.Oelschlaeger, and A.Warshel (2010).
A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.
  Proteins, 78, 671-680.  
20844920 S.H.Wilson, W.A.Beard, D.D.Shock, V.K.Batra, N.A.Cavanaugh, R.Prasad, E.W.Hou, Y.Liu, K.Asagoshi, J.K.Horton, D.F.Stefanick, P.S.Kedar, M.J.Carrozza, A.Masaoka, and M.L.Heacock (2010).
Base excision repair and design of small molecule inhibitors of human DNA polymerase β.
  Cell Mol Life Sci, 67, 3633-3647.  
20526335 V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, and S.H.Wilson (2010).
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site.
  Nat Struct Mol Biol, 17, 889-890.
PDB code: 3mby
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
19013261 G.C.Lin, J.Jaeger, K.A.Eckert, and J.B.Sweasy (2009).
Loop II of DNA polymerase beta is important for discrimination during substrate binding.
  DNA Repair (Amst), 8, 182-189.  
19619136 H.Li, R.Swiercz, and E.W.Englander (2009).
Elevated metals compromise repair of oxidative DNA damage via the base excision repair pathway: implications of pathologic iron overload in the brain on integrity of neuronal DNA.
  J Neurochem, 110, 1774-1783.  
19560423 J.F.Sydow, F.Brueckner, A.C.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, and P.Cramer (2009).
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
  Mol Cell, 34, 710-721.
PDB codes: 3hou 3hov 3how 3hox 3hoy 3hoz
19572669 M.C.Foley, and T.Schlick (2009).
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates.
  J Phys Chem B, 113, 13035-13047.  
19351147 T.G.Upton, B.A.Kashemirov, C.E.McKenna, M.F.Goodman, G.K.Prakash, R.Kultyshev, V.K.Batra, D.D.Shock, L.C.Pedersen, W.A.Beard, and S.H.Wilson (2009).
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function.
  Org Lett, 11, 1883-1886.
PDB code: 3gdx
19759017 W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, and S.H.Wilson (2009).
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
  J Biol Chem, 284, 31680-31689.
PDB codes: 3isb 3isc 3isd
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
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 codes are shown on the right.