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: 74.82 kDa 
• Atom Count: 5533 
• Modelled Residue Count: 602 
• Deposited Residue Count: 605 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1XC9

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

• PDB DOI: 10.2210/pdb1XC9/pdb
• NDB: PD0593

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


• Deposited: 2004-09-01 Released: 2004-12-14 
• Deposition Author(s): Hsu, G.W., Huang, X., Luneva, N.P., Geacintov, N.E., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication

Hsu, G.W., Huang, X., Luneva, N.P., Geacintov, N.E., Beese, L.S.

(2005) J Biol Chem 280: 3764-3770

• PubMed: 15548515 
• DOI: 10.1074/jbc.M411276200
• Primary Citation of Related Structures:  
  1XC9


• PubMed Abstract: 
  

Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to various human cancers, particularly lung and skin. BP is metabolized to diol epoxides that covalently modify DNA bases to form bulky adducts that block DNA synthesis by replicative or high fidelity DNA polymerases. Here we present the structure of a high fidelity polymerase from a thermostable strain of Bacillus stearothermophilus (Bacillus fragment) bound to the most common BP-derived N2-guanine adduct base-paired with cytosine. The BP adduct adopts a conformation that places the polycyclic BP moiety in the nascent DNA minor groove and is the first structure of a minor groove adduct bound to a polymerase. Orientation of the BP moiety into the nascent DNA minor groove results in extensive disruption to the interactions between the adducted DNA duplex and the polymerase. The disruptions revealed by the structure of Bacillus fragment bound to a BP adduct provide a molecular basis for rationalizing the potent blocking effect on replication exerted by BP adducts.

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Related Citations: 

• Observing translation synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase
  Hsu, G.W., Kiefer, J.R., Becherel, O.J., Fuchs, R.P.P., Beese, L.S.
  () To be published --: --

• 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, 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  Gene Names: polA, pol EC: 2.7.7.7
UniProt
Find proteins for P52026 (Geobacillus stearothermophilus) Explore P52026  Go to UniProtKB:  P52026

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 benzo[a]pyrene adduct	B [auth C]	15	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAP	E [auth C]	1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE C20 H16 O3 GFANZDFKCCJYRF-NSISKUIASA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.752	α = 90
b = 93.733	β = 90
c = 104.512	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: 2004-09-01 
• Released Date: 2004-12-14 
Deposition Author(s): Hsu, G.W., Huang, X., Luneva, N.P., Geacintov, N.E., Beese, L.S.

Revision History  

• Version 1.0: 2004-12-14
  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