Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72406.16 
• Atom Count: 5061 
• Residue Count: 600 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2Y1J

CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS

• DOI: 10.2210/pdb2Y1J/pdb
• NDB: NA1232

• Classification: TRANSFERASE/DNA
• Organism(s): synthetic construct, Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2010-12-08 Released: 2011-07-27 
• Deposition Author(s): Heil, K., Schneider, S., Mueller, M., Kneuttinger, A.C., Carell, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 

Literature

Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion.

Heil, K., Kneuttinger, A.C., Schneider, S., Lischke, U., Carell, T.

(2011) Chemistry 17: 9651

• PubMed: 21780197 
• DOI: 10.1002/chem.201100177
• Primary Citation of Related Structures:  
  2Y1I


• PubMed Abstract: 
  

UV light is one of the major causes of DNA damage. In spore DNA, due to an unusual packing of the genetic material, a special spore photoproduct lesion (SP lesion) is formed, which is repaired by the enzyme spore photoproduct lyase (Spl), a radical S-adenosylmethionine (SAM) enzyme. We report here the synthesis and DNA incorporation of a DNA SP lesion analogue lacking the phosphodiester backbone. The oligonucleotides were used for repair studies and they were cocrystallized with a polymerase enzyme as a template to clarify the configuration of the SP lesion and to provide information about the base-pairing properties of the lesion. The structural analysis together with repair studies allowed us to clarify the identity of the preferentially repaired lesion diastereoisomer.

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Organizational Affiliation: 

Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Munich, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERASE I	A	580	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: polA EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Go to UniProtKB:  E1C9K5

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'	B	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*AP*GP*GP*GP*QBTP*THM*GP*GP*TP*CP)-3'	C	10	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
QBT	C	DNA LINKING	C10 H17 N2 O8 P		T
THM	C	DNA OH 5 prime terminus	C10 H14 N2 O5		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 88.525	α = 90.00
b = 93.382	β = 90.00
c = 105.773	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
XDS	data reduction
SCALA	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-08 
• Released Date: 2011-07-27 
• Deposition Author(s): Heil, K., Schneider, S., Mueller, M., Kneuttinger, A.C., Carell, T.

Revision History 

• Version 1.0: 2011-07-27
  Type: Initial release
• Version 1.1: 2011-11-02
  Type: Database references