Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.16 kDa 
• Atom Count: 5438 
• Modelled Residue Count: 601 
• Deposited Residue Count: 604 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1UA0

Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase

• PDB DOI: 10.2210/pdb1UA0/pdb
• NDB: PD0585

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


• Deposited: 2004-08-11 Released: 2004-09-28 
• Deposition Author(s): Hsu, G.W., Kiefer, J.R., Becherel, O.J., Fuchs, R.P.P., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase

Hsu, G.W., Kiefer, J.R., Burnouf, D., Becherel, O.J., Fuchs, R.P.P., Beese, L.S.

(2004) J Biol Chem 279: 50280-50285

• PubMed: 15385534 
• DOI: 10.1074/jbc.M409224200
• Primary Citation of Related Structures:  
  1UA0, 1UA1


• PubMed Abstract: 
  

Aromatic amines have been studied for more than a half-century as model carcinogens representing a class of chemicals that form bulky adducts to the C8 position of guanine in DNA. Among these guanine adducts, the N-(2'-deoxyguanosin-8-yl)-aminofluorene (G-AF) and N-2-(2'-deoxyguanosin-8-yl)-acetylaminofluorene (G-AAF) derivatives are the best studied. Although G-AF and G-AAF differ by only an acetyl group, they exert different effects on DNA replication by replicative and high-fidelity DNA polymerases. Translesion synthesis of G-AF is achieved with high-fidelity polymerases, whereas replication of G-AAF requires specialized bypass polymerases. Here we have presented structures of G-AF as it undergoes one round of accurate replication by a high-fidelity DNA polymerase. Nucleotide incorporation opposite G-AF is achieved in solution and in the crystal, revealing how the polymerase accommodates and replicates past G-AF, but not G-AAF. Like an unmodified guanine, G-AF adopts a conformation that allows it to form Watson-Crick hydrogen bonds with an opposing cytosine that results in protrusion of the bulky fluorene moiety into the major groove. Although incorporation opposite G-AF is observed, the C:G-AF base pair induces distortions to the polymerase active site that slow translesion synthesis.

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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

• Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
  Johnson, S.J., Taylor, J.S., Beese, L.S.
  (2003) Proc Natl Acad Sci U S A 100: 3895

• Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
  Kiefer, J.R., Mao, C., Braman, J.C., Beese, L.S.
  (1998) Nature 391: 304

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I	C [auth A]	580	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KWC1  Go to UniProtKB:  Q5KWC1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA primer strand	A [auth B]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA template strand with aminofluorene adduct	B [auth C]	14	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
AF	E [auth C]	2-AMINOFLUORENE C13 H11 N CFRFHWQYWJMEJN-UHFFFAOYSA-N
SO4	F [auth A], G [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: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.868	α = 90
b = 93.471	β = 90
c = 104.656	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-11 
• Released Date: 2004-09-28 
Deposition Author(s): Hsu, G.W., Kiefer, J.R., Becherel, O.J., Fuchs, R.P.P., Beese, L.S.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary