7KT6 | pdb_00007kt6

DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 10 mM Mn2+ (960min)

• PDB DOI: https://doi.org/10.2210/pdb7KT6/pdb
• NAKB: 7KT6

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-24 Released: 2021-12-15 
• Deposition Author(s): Jamsen, J.A., Wilson, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

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

• PubMed: 33824325 
• DOI: https://doi.org/10.1038/s41467-021-21354-6
• Primary Citation 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.

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Organizational Affiliation: 
• Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
Laboratory of Chromatin Metabolism and Epigenetics, Graduate School of Science, Chiba University, Chiba, Japan.
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.53 kDa 
• Atom Count: 3,429 
• Modeled Residue Count: 343 
• Deposited Residue Count: 374 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed DNA/RNA polymerase mu	A	356	Homo sapiens	Mutation(s): 0  Gene Names: POLM, polmu 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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')	B [auth T]	9	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')	C [auth P]	5	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*CP*G)-3')	D	4	Homo sapiens

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	O [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
DTT	K [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
GOA (Subject of Investigation/LOI)	P [auth A]	GLYCOLIC ACID C2 H4 O3 AEMRFAOFKBGASW-UHFFFAOYSA-N
EDO	L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth T]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.081	α = 90
b = 68.692	β = 90
c = 110.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Jamsen, J.A., Wilson, S.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	Z01-ES050158
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	Z01-ES050161
Japan Society for the Promotion of Science (JSPS)	Japan	16K16195

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations