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PDBsum entry 1zjm

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protein dna_rna metals links
DNA/lyase/transferase PDB id
1zjm
Jmol
Contents
Protein chain
323 a.a. *
DNA/RNA
Metals
_NA ×3
Waters ×344
* Residue conservation analysis
PDB id:
1zjm
Name: DNA/lyase/transferase
Title: Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus
Structure: D( Cp Cp Gp Ap Cp Cp Ap 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 A)-3'. Chain: p. Engineered: yes. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.228     R-free:   0.234
Authors: V.K.Batra,W.A.Beard,D.D.Shock,L.C.Pedersen,S.H.Wilson
Key ref:
V.K.Batra et al. (2005). Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Structure (Camb), 13, 1225-1233. PubMed id: 16084394 DOI: 10.1016/j.str.2005.05.010
Date:
29-Apr-05     Release date:   16-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
Seq:
Struc:
335 a.a.
323 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
+ 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  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2005.05.010 Structure (Camb) 13:1225-1233 (2005)
PubMed id: 16084394  
 
 
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.
V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson.
 
  ABSTRACT  
 
DNA polymerases occasionally insert the wrong nucleotide. For this error to become a mutation, the mispair must be extended. We report a structure of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase active site. The structure of this complex indicates that the templating adenine of the mispair stacks with the primer terminus adenine while the templating (coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the binary complex with dGTP resulted in crystals of a ternary substrate complex. In this case, the templating cytosine is observed within the DNA helix and forms Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out of position for efficient nucleotide insertion.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Structural Comparison of the Binary DNA and Ternary Substrate Complexes of DNA Polymerase b with an A-A Mismatch at the Boundary of the Active Site
A comparison of the polymerase and DNA conformations near the polymerase active site in the crystallographic structures of the binary (blue) and ternary (green) complexes with an A-A mismatch (yellow) at the primer terminus. As with matched termini, the N subdomain is observed to be open in the binary complex and closed in the ternary complex. Three striking conformational changes in the DNA are observed in forming the closed ternary substrate complex: (1) the adenine at the primer terminus rotates into a syn-conformation; (2) this permits the templating adenine of the mismatch to reposition itself opposite the primer terminus (n -1); (3) the coding template cytosine (orange) flips into the DNA helix, thereby forming Watson-Crick hydrogen bonds with the incoming dGTP (orange).
 
  The above figure is reprinted by permission from Cell Press: Structure (Camb) (2005, 13, 1225-1233) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
18955064 B.A.Sampoli Benítez, K.Arora, L.Balistreri, and T.Schlick (2008).
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation.
  J Mol Biol, 384, 1086-1097.  
18616290 D.L.Murphy, J.Kosa, J.Jaeger, and J.B.Sweasy (2008).
The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding.
  Biochemistry, 47, 8048-8057.  
18385153 K.H.Tang, M.Niebuhr, C.S.Tung, H.C.Chan, C.C.Chou, and M.D.Tsai (2008).
Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.
  Nucleic Acids Res, 36, 2948-2957.
PDB code: 2van
18717589 M.P.Roettger, M.Bakhtina, and M.D.Tsai (2008).
Mismatched and matched dNTP incorporation by DNA polymerase beta proceed via analogous kinetic pathways.
  Biochemistry, 47, 9718-9727.  
18471977 V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, and S.H.Wilson (2008).
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
  Mol Cell, 30, 315-324.
PDB codes: 3c2k 3c2l 3c2m
17631059 A.F.Moon, M.Garcia-Diaz, V.K.Batra, W.A.Beard, K.Bebenek, T.A.Kunkel, S.H.Wilson, and L.C.Pedersen (2007).
The X family portrait: structural insights into biological functions of X family polymerases.
  DNA Repair (Amst), 6, 1709-1725.  
17293403 Y.Wang, S.Reddy, W.A.Beard, S.H.Wilson, and T.Schlick (2007).
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.
  Biophys J, 92, 3063-3070.  
17176036 R.Radhakrishnan, K.Arora, Y.Wang, W.A.Beard, S.H.Wilson, and T.Schlick (2006).
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.
  Biochemistry, 45, 15142-15156.  
16615916 V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, and S.H.Wilson (2006).
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
  Structure, 14, 757-766.
PDB codes: 2fmp 2fmq 2fms
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.