Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101.33 kDa 
• Atom Count: 6485 
• Residue Count: 770 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2XHB

Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA

• DOI: 10.2210/pdb2XHB/pdb
• NDB: NA0623

• Classification: TRANSFERASE/DNA
• Organism(s): Thermococcus gorgonarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-06-14 Released: 2010-07-21 
• Deposition Author(s): Killelea, T., Ghosh, S., Tan, S.S., Heslop, P., Firbank, S.J., Kool, E.T., Connolly, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.295 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 

Literature

Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-Ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues.

Killelea, T., Ghosh, S., Tan, S.S., Heslop, P., Firbank, S.J., Kool, E.T., Connolly, B.A.

(2010) Biochemistry 49: 5772

• PubMed: 20527806 
• DOI: 10.1021/bi100421r
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describe uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at position 2 explains the stimulation of the polymerase 3'-5' proofreading exonuclease, observed with deaminated bases at this location. A beta-hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double-stranded DNA. This denatures the two complementary primer bases and directs the resulting 3' single-stranded extension toward the exonuclease active site. Finally, the relative importance of hydrogen bonding and shape fit in determining selectivity for deaminated bases has been examined using nonpolar isosteres. Affinity for both 2,4-difluorobenzene and fluorobenzimidazole, non-hydrogen bonding shape mimics of uracil and hypoxanthine, respectively, is strongly diminished, suggesting polar protein-base contacts are important. However, residual interaction with 2,4-difluorobenzene is seen, confirming a role for shape recognition.

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Organizational Affiliation: 

Institute of Cell and Molecular Biosciences (ICaMB), The University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERASE	A	773	Thermococcus gorgonarius	Mutation(s): 1  Gene Names: pol, polA EC: 2.7.7.7
Find proteins for P56689 (Thermococcus gorgonarius) Go to UniProtKB:  P56689

Entity ID: 2
Molecule	Chains	Length	Organism
HYPOXANTHINE-CONTAINING DNA	D	28	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'	E	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.295 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.45	α = 90
b = 98.37	β = 90
c = 116.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-14 
• Released Date: 2010-07-21 
Deposition Author(s): Killelea, T., Ghosh, S., Tan, S.S., Heslop, P., Firbank, S.J., Kool, E.T., Connolly, B.A.

Revision History 

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance