2Y1J image
Deposition Date 2010-12-08
Release Date 2011-07-27
Last Version Date 2023-12-20
Entry Detail
PDB ID:
2Y1J
Keywords:
TRANSFERASE/DNA
Title:
CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
Biological Source:
Source Organism:
GEOBACILLUS STEAROTHERMOPHILUS (Taxon ID: 1422)
SYNTHETIC CONSTRUCT (Taxon ID: 32630)
Host Organism:
ESCHERICHIA COLI
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.15 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 21 21 21
2Y1J validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA POLYMERASE I
Chain IDs:A
Chain Length:580
Number of Molecules:1
Biological Source:GEOBACILLUS STEAROTHERMOPHILUS
UniProt ID:E1C9K5 Pfam ID:PF22619, PF00476
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'
Chain IDs:B
Chain Length:10
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*GP*GP*GP*QBTP*THM*GP*GP*TP*CP)-3'
Chain IDs:C
Chain Length:10
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
QBT C T ?
Ligand Molecules
SO4
Primary Citation
Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion.
Chemistry 17 9651 ? (2011)
PMID: 21780197 DOI: 10.1002/CHEM.201100177

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
2Y1I