4NY8

DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.246 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta.

Koag, M.C.Lee, S.

(2014) J.Am.Chem.Soc. 136: 5709-5721

  • DOI: 10.1021/ja500172d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human DNA polymerase β (polβ) inserts, albeit slowly, T opposite the carcinogenic lesion O6-methylguanine (O6MeG) ∼30-fold more frequently than C. To gain insight into this promutagenic process, we solved four ternary structures of polβ with an incom ...

    Human DNA polymerase β (polβ) inserts, albeit slowly, T opposite the carcinogenic lesion O6-methylguanine (O6MeG) ∼30-fold more frequently than C. To gain insight into this promutagenic process, we solved four ternary structures of polβ with an incoming dCTP or dTTP analogue base-paired with O6MeG in the presence of active-site Mg(2+) or Mn(2+). The Mg(2+)-bound structures show that both the O6MeG·dCTP/dTTP-Mg(2+) complexes adopt an open protein conformation, staggered base pair, and one active-site metal ion. The Mn(2+)-bound structures reveal that, whereas the O6Me·dCTP-Mn(2+) complex assumes the similar altered conformation, the O6MeG·dTTP-Mn(2+) complex adopts a catalytically competent state with a closed protein conformation and pseudo-Watson-Crick base pair. On the basis of these observations, we conclude that polβ slows nucleotide incorporation opposite O6MeG by inducing an altered conformation suboptimal for catalysis and promotes mutagenic replication by allowing Watson-Crick-mode for O6MeG·T but not for O6MeG·C in the enzyme active site. The O6MeG·dTTP-Mn(2+) ternary structure, which represents the first structure of mismatched polβ ternary complex with a closed protein conformation and coplanar base pair, the first structure of pseudo-Watson-Crick O6MeG·T formed in the active site of a DNA polymerase, and a rare, if not the first, example of metal-dependent conformational activation of a DNA polymerase, indicate that catalytic metal-ion coordination is utilized as a kinetic checkpoint by polβ and is crucial for the conformational activation of polβ. Overall, our structural studies not only explain the promutagenic polβ catalysis across O6MeG but also provide new insights into the replication fidelity of polβ.


    Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
326Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'T16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'P10N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*GP*TP*CP*GP*G)-3'D5N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
0KX
Query on 0KX

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Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
C9 H17 N4 O12 P3
STYMTWKSQLVXJN-SHYZEUOFSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6OG
Query on 6OG
T
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.246 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.625α = 90.00
b = 79.288β = 105.97
c = 54.838γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
StructureStudiodata collection
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references