PDBsum entry 2y1j

Transferase/DNA

PDB id: 2y1j

Contents

Protein chain

580 a.a.

DNA/RNA

Ligands

SO4 ×2

Waters ×167

PDB id:

2y1j

Name:

Transferase/DNA

Title:

Crystal structure of a r-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase i from bacillus stearothermophilus

Structure:

DNA polymerase i. Chain: a. Fragment: residues 297-876. Engineered: yes. 5'-d( Gp Ap Cp Cp Ap Ap Cp Cp Cp Tp)-3'. Chain: b. Engineered: yes. 5'-d( Ap Gp Gp Gp Qbtp Thm Gp Gp Tp Cp)-3'. Chain: c.

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: dsm 22. Atcc: 12980. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: german collection of microorganisms (dsm). Synthetic: yes. Synthetic construct.

Resolution:

2.15Å R-factor: 0.201 R-free: 0.241

Authors:

K.Heil,S.Schneider,M.Mueller,A.C.Kneuttinger,T.Carell

Key ref:

K.Heil et al. (2011). Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion. Chemistry, 17, 9651-9657. PubMed id: 21780197

Date:

08-Dec-10 Release date: 27-Jul-11

Protein chain

E1C9K5  (E1C9K5_GEOSE) -  DNA polymerase I from Geobacillus stearothermophilus

Seq: 580 a.a.

Struc: 580 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

G-A-C-C-A-A-C-C-C-T 10 bases

A-G-G-G-QBT-THM-G-G-T-C 10 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Chemistry 17:9651-9657 (2011)

PubMed id: 21780197

Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion.

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

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.