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: 76.67 kDa 
• Atom Count: 6,036 
• Modelled Residue Count: 601 
• Deposited Residue Count: 618 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3TAN

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-1) Position

• PDB DOI:  https://doi.org/10.2210/pdb3TAN/pdb
• NDB: NA1272

• Classification: TRANSFERASE/DNA
• Organism(s): Geobacillus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-04 Released: 2011-10-19 
• Deposition Author(s): Wang, W., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.184 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 

Literature

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.

Wang, W., Hellinga, H.W., Beese, L.S.

(2011) Proc Natl Acad Sci U S A 108: 17644-17648

• PubMed: 22006298 
• DOI: https://doi.org/10.1073/pnas.1114496108
• Primary Citation of Related Structures:  
  3PV8, 3PX0, 3PX4, 3PX6, 3TAN, 3TAP, 3TAQ, 3TAR, 3THV, 3TI0


• PubMed Abstract: 
  

Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C • A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.

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Related Citations: 

• Structures of mismatch replication errors observed in a DNA polymerase.
  Johnson, S.J., Beese, L.S.
  (2004) Cell 116: 803

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Organizational Affiliation: 

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I	A	592	Geobacillus	Mutation(s): 0  EC: 2.7.7.7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*C)-3'	B	10	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*CP*GP*T*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'	C	16	N/A

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
DCP	I [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.184 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.43	α = 90
b = 93.01	β = 90
c = 105.33	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Wang, W., Beese, L.S.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Database references
• Version 1.2: 2014-04-02
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary