4YMN

Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.591 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication.

Kou, Y.Koag, M.C.Lee, S.

(2018) Biochemistry --: --

  • DOI: 10.1021/acs.biochem.8b00331
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A wide variety of endogenous and exogenous alkylating agents attack DNA to preferentially generate N7-alkylguanine (N7-alkylG) adducts. Studies of the effect of N7-alkylG lesions on biological processes have been difficult in part because of complica ...

    A wide variety of endogenous and exogenous alkylating agents attack DNA to preferentially generate N7-alkylguanine (N7-alkylG) adducts. Studies of the effect of N7-alkylG lesions on biological processes have been difficult in part because of complications arising from the chemical lability of the positively charged N7-alkylG, which can readily produce secondary lesions. To assess the effect of bulky N7-alkylG on DNA replication, we prepared chemically stable N7-benzylguanine (N7bnG)-containing DNA and evaluated nucleotide incorporation opposite the lesion by human DNA polymerase β (polβ), a model enzyme for high-fidelity DNA polymerases. Kinetic studies showed that the N7-benzyl-G lesion greatly inhibited dCTP incorporation by polβ. The crystal structure of polβ incorporating dCTP opposite N7bnG showed a Watson-Crick N7bnG:dCTP structure. The polβ-N7bnG:dCTP structure showed an open protein conformation, a relatively disordered dCTP, and a lack of catalytic metal, which explained the inefficient nucleotide incorporation opposite N7bnG. This indicates that polβ is sensitive to major groove adducts in the templating base side and deters nucleotide incorporation opposite bulky N7-alkylG adducts by adopting a catalytically incompetent conformation. Substituting Mg 2+ for Mn 2+ induced an open-to-closed conformational change due to the presence of catalytic metal and stably bound dCTP and increased the catalytic efficiency by ∼10-fold, highlighting the effect of binding of the incoming nucleotide and catalytic metal on protein conformation and nucleotidyl transfer reaction. Overall, these results suggest that, although bulky alkyl groups at guanine-N7 may not alter base pairing properties of guanine, the major groove-positioned lesions in the template could impede nucleotidyl transfer by some DNA polymerases.


    Organizational Affiliation

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




Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo 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
DNA 16-mer (template)T16Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA 10-mer (up-primer)P10Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
DNA 5-mer (dn-primer)D5Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KX
Query on 0KX

Download SDF File 
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
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
7BG
Query on 7BG
T
DNA linkingC17 H20 F N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.591 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.907α = 90.00
b = 79.020β = 107.92
c = 55.019γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-03-06 
  • Released Date: 2016-03-09 
  • Deposition Author(s): Lee, S., Koag, M.-C.

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references, Derived calculations