1SKS | pdb_00001sks

Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template

• PDB DOI: https://doi.org/10.2210/pdb1SKS/pdb
• NAKB: 1SKS

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


• Deposited: 2004-03-05 Released: 2004-07-06 
• Deposition Author(s): Li, Y., Dutta, S., Doublie, S., Bdour, H.M., Taylor, J.S., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.

Li, Y., Dutta, S., Doublie, S., Bdour, H.M., Taylor, J.S., Ellenberger, T.

(2004) Nat Struct Mol Biol 11: 784-790

• PubMed: 15235589 
• DOI: https://doi.org/10.1038/nsmb792
• Primary Citation Related Structures: 
  1SKR, 1SKS, 1SKW, 1SL0, 1SL1, 1SL2


• PubMed Abstract: 
  

  Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 105.15 kDa 
• Atom Count: 6,769 
• Modeled Residue Count: 809 
• Deposited Residue Count: 852 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

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, B3781, C4701, Z5291, ECS4714, STM3915, STMD1.75, STY3639, T3381, SF3854, S3905
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(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3'	A [auth P]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3'	B [auth T]	25	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: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.773	α = 90
b = 214.917	β = 90
c = 52.257	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-06 
Deposition Author(s): Li, Y., Dutta, S., Doublie, S., Bdour, H.M., Taylor, J.S., Ellenberger, T.

Revision History  

• Version 1.0: 2004-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Structure summary