Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 105.71 kDa 
• Atom Count: 6824 
• Modelled Residue Count: 802 
• Deposited Residue Count: 854 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1X9M

T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA

• PDB DOI: 10.2210/pdb1X9M/pdb
• NDB: PD0589

• Classification: TRANSFERASE/ELECTRON TRANSPORT/DNA
• Organism(s): Escherichia phage T7, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-23 Released: 2004-10-26 
• Deposition Author(s): Dutta, S., Li, Y., Johnson, D., Dzantiev, L., Richardson, C.C., Romano, L.J., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Literature

Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.

Dutta, S., Li, Y., Johnson, D., Dzantiev, L., Richardson, C.C., Romano, L.J., Ellenberger, T.

(2004) Proc Natl Acad Sci U S A 101: 16186-16191

• PubMed: 15528277 
• DOI: 10.1073/pnas.0406516101
• Primary Citation of Related Structures:  
  1X9M, 1X9S, 1X9W


• PubMed Abstract: 
  

The carcinogen 2-acetylaminofluorene forms two major DNA adducts: N-(2'-deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) and its deacetylated derivative, N-(2'-deoxyguanosin-8-yl)-2-aminofluorene (dG-AF). Although the dG-AAF and dG-AF adducts are distinguished only by the presence or absence of an acetyl group, they have profoundly different effects on DNA replication. dG-AAF poses a strong block to DNA synthesis and primarily induces frameshift mutations in bacteria, resulting in the loss of one or two nucleotides during replication past the lesion. dG-AF is less toxic and more easily bypassed by DNA polymerases, albeit with an increased frequency of misincorporation opposite the lesion, primarily resulting in G --> T transversions. We present three crystal structures of bacteriophage T7 DNA polymerase replication complexes, one with dG-AAF in the templating position and two others with dG-AF in the templating position. Our crystallographic data suggest why a dG-AAF adduct blocks replication more strongly than does a dG-AF adduct and provide a possible explanation for frameshift mutagenesis during replication bypass of a dG-AAF adduct. The dG-AAF nucleoside adopts a syn conformation that facilitates the intercalation of its fluorene ring into a hydrophobic pocket on the surface of the fingers subdomain and locks the fingers in an open, inactive conformation. In contrast, the dG-AF base at the templating position is not well defined by the electron density, consistent with weak binding to the polymerase and a possible interchange of this adduct between the syn and anti conformations.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	C [auth A]	698	Escherichia phage T7	Mutation(s): 0  Gene Names: 5 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P00581 (Escherichia phage T7) Explore P00581  Go to UniProtKB:  P00581

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1	D [auth B]	108	Escherichia coli	Mutation(s): 0  Gene Names: trxA, tsnC, fipA
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*TP*GP*GP*TP*AP*GP*TP*GP*TP*GP*AP*(2DT))-3'	A [auth C]	22	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*CP*(8FG)P*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3'	B [auth D]	26	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.109	α = 90
b = 212.308	β = 90
c = 52.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-23 
• Released Date: 2004-10-26 
Deposition Author(s): Dutta, S., Li, Y., Johnson, D., Dzantiev, L., Richardson, C.C., Romano, L.J., Ellenberger, T.

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance