RCSB PDB - 7KTM: DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (30min)

 7KTM

DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (30min)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8DGClick on this verticalbar to view detailsBest fitted PPVClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide.

Jamsen, J.A.Sassa, A.Shock, D.D.Beard, W.A.Wilson, S.H.

(2021) Nat Commun 12: 2059-2059

  • DOI: https://doi.org/10.1038/s41467-021-21354-6
  • Primary Citation of Related Structures:  
    7KSS, 7KST, 7KSU, 7KSV, 7KSW, 7KSX, 7KSY, 7KSZ, 7KT0, 7KT1, 7KT2, 7KT3, 7KT4, 7KT5, 7KT6, 7KT7, 7KT8, 7KT9, 7KTA, 7KTB, 7KTC, 7KTD, 7KTE, 7KTF, 7KTG, 7KTH, 7KTI, 7KTJ, 7KTK, 7KTL, 7KTM, 7KTN

  • PubMed Abstract: 

    Oxidized dGTP (8-oxo-7,8-dihydro-2´-deoxyguanosine triphosphate, 8-oxodGTP) insertion by DNA polymerases strongly promotes cancer and human disease. How DNA polymerases discriminate against oxidized and undamaged nucleotides, especially in error-prone double strand break (DSB) repair, is poorly understood. High-resolution time-lapse X-ray crystallography snapshots of DSB repair polymerase μ undergoing DNA synthesis reveal that a third active site metal promotes insertion of oxidized and undamaged dGTP in the canonical anti-conformation opposite template cytosine. The product metal bridged O8 with product oxygens, and was not observed in the syn-conformation opposite template adenine (A t ). Rotation of A t into the syn-conformation enabled undamaged dGTP misinsertion. Exploiting metal and substrate dynamics in a rigid active site allows 8-oxodGTP to circumvent polymerase fidelity safeguards to promote pro-mutagenic double strand break repair.


  • Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed DNA/RNA polymerase mu356Homo sapiensMutation(s): 1 
Gene Names: POLMpolmu
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP87 (Homo sapiens)
Explore Q9NP87 
Go to UniProtKB:  Q9NP87
PHAROS:  Q9NP87
GTEx:  ENSG00000122678 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP87
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8DG (Subject of Investigation/LOI)
Query on 8DG

Download Ideal Coordinates CCD File 
K [auth A]8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
BUZOGVVQWCXXDP-VPENINKCSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
Q [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PPV (Subject of Investigation/LOI)
Query on PPV

Download Ideal Coordinates CCD File 
L [auth A]PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A],
P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.241α = 90
b = 62.223β = 90
c = 118.797γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8DGClick on this verticalbar to view detailsBest fitted PPVClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01-ES050158
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01-ES050161
Japan Society for the Promotion of Science (JSPS)Japan16K16195

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description