3C2M

Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.

Batra, V.K.Beard, W.A.Shock, D.D.Pedersen, L.C.Wilson, S.H.

(2008) Mol Cell 30: 315-324

  • DOI: 10.1016/j.molcel.2008.02.025
  • Primary Citation of Related Structures:  
    3C2K, 3C2L, 3C2M

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaD [auth A]335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
GTEx:  ENSG00000070501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06746
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DGP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3')A [auth T]16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3')B [auth P]10N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DGP*DTP*DCP*DGP*DG)-3')C [auth D]5N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F2A
Query on F2A

Download Ideal Coordinates CCD File 
S [auth A]2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
C11 H18 N5 O11 P3
XETARULVTCYJAN-XLPZGREQSA-N
 Ligand Interaction
EDO
Query on EDO

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H [auth D],
T [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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E [auth T],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
E [auth T],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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F [auth T],
G [auth P],
O [auth A],
P [auth A],
Q [auth A],
F [auth T],
G [auth P],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F2A BindingDB:  3C2M Ki: 5000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.75α = 90
b = 78.37β = 113.36
c = 55.17γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance