4B9S | pdb_00004b9s

Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion outside of the pre-insertion site.

• PDB DOI: https://doi.org/10.2210/pdb4B9S/pdb
• NAKB: 4B9S

• Classification: TRANSFERASE/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-09-06 Released: 2013-04-17 
• Deposition Author(s): Gehrke, T.H., Lischke, U., Arnold, S., Schneider, S., Carell, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions.

Gehrke, T.H., Lischke, U., Gasteiger, K.L., Schneider, S., Arnold, S., Muller, H.C., Stephenson, D.S., Zipse, H., Carell, T.

(2013) Nat Chem Biol 9: 455

• PubMed: 23685671 
• DOI: https://doi.org/10.1038/nchembio.1254
• Primary Citation Related Structures: 
  4B9L, 4B9M, 4B9N, 4B9S, 4B9T, 4B9U, 4B9V


• PubMed Abstract: 
  

  8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1' glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming triphosphates during DNA replication. Here we present biochemical data and what are to our knowledge the first crystal structures of carbocyclic FaPydA and FaPydG containing DNA in complex with a high-fidelity polymerase. Crystallographic snapshots show that the cFaPy lesions keep the anti geometry of the glycosidic bond during error-free and error-prone replication. The observed dG·dC→dT·dA transversion mutations are the result of base shifting and tautomerization.

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Organizational Affiliation: 
• Center for Integrated Protein Science at the Department of Chemistry, Ludwig Maximilians University, Munich, Germany.

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: 78.94 kDa 
• Atom Count: 5,474 
• Modeled Residue Count: 601 
• Deposited Residue Count: 644 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE	A	619	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5  Go to UniProtKB:  E1C9K5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'	B	10	Geobacillus stearothermophilus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*TP*TP)-3'	C	15	Geobacillus stearothermophilus

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	D	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.066	α = 90
b = 93.688	β = 90
c = 105.604	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Gehrke, T.H., Lischke, U., Arnold, S., Schneider, S., Carell, T.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references, Structure summary
• Version 1.2: 2013-05-29
  Changes: Database references
• Version 1.3: 2013-07-03
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary