2XCA

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM

• PDB DOI: https://doi.org/10.2210/pdb2XCA/pdb
• NAKB: 2XCA

• Classification: TRANSFERASE/DNA
• Organism(s): Saccharolobus solfataricus P2, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-20 Released: 2010-09-08 
• Deposition Author(s): Irimia, A., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus

Irimia, A., Loukachevitch, L.V., Eoff, R.L., Guengerich, F.P., Egli, M.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1013

• PubMed: 20823515 
• DOI: https://doi.org/10.1107/S1744309110029374
• Primary Citation of Related Structures:  
  2XC9, 2XCA, 2XCP


• PubMed Abstract: 
  

  Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.

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Organizational Affiliation: 

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, USA.

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: 51.16 kDa 
• Atom Count: 3,590 
• Modelled Residue Count: 372 
• Deposited Residue Count: 389 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE IV	A	358	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: DPO4 EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02  Go to UniProtKB:  Q97W02

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*DOC)-3'	B [auth P]	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP*TP*CP* CP*CP*CP*C)-3'	C [auth T]	18	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	D [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG	E [auth A], F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.443	α = 90
b = 103.909	β = 90
c = 52.707	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Irimia, A., Egli, M.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references, Refinement description, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description