PDBsum entry 2wb2

Lyase/DNA

PDB id: 2wb2

Contents

Protein chain

508 a.a. *

DNA/RNA

Ligands

FAD

* Residue conservation analysis

PDB id:

2wb2

Name:

Lyase/DNA

Title:

Drosophila melanogaster (6-4) photolyase bound to double stranded DNA containing a t(6-4)c photolesion

Structure:

Photolyase. Chain: a. Fragment: residues 1-520. Synonym: DNA photolyase, re11660p. Engineered: yes. 5'-d( Ap Cp Ap Gp Cp Gp Gp 64Pp Zp Gp Cp Ap Gp Gp T)-3'. Chain: c. Engineered: yes. Other_details: 6-4 link between t 8 and c 8 (see remark 600).

Source:

Drosophila melanogaster. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 83333. Expression_system_variant: rosetta-gami plyss (de3). Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.95Å R-factor: 0.206 R-free: 0.243

Authors:

A.F.Glas,S.Schneider,M.J.Maul,U.Hennecke,T.Carell

Key ref:

A.F.Glas et al. (2009). Crystal structure of the T(6-4)C lesion in complex with a (6-4) DNA photolyase and repair of UV-induced (6-4) and Dewar photolesions. Chemistry, 15, 10387-10396. PubMed id: 19722240

Date:

20-Feb-09 Release date: 17-Mar-09

Protein chain

Q8SXK5  (Q8SXK5_DROME) -  Cryptochrome-1 from Drosophila melanogaster

Seq: 540 a.a.

Struc: 508 a.a.

DNA/RNA chains

A-C-A-G-C-G-G-64P-__Z-G-C-A-G-G-T 15 bases

T-A-C-C-T-G-C-G-A-C-C-G-C-T-G 15 bases

Enzyme reactions

• Enzyme class: E.C.4.1.99.3 - deoxyribodipyrimidine photo-lyase.
• Pathway: EC 4.1.99.3
• Reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
• Cofactor: 5,10-methenyltetrahydrofolate; FAD

5,10-methenyltetrahydrofolate FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

reference

Chemistry 15:10387-10396 (2009)

PubMed id: 19722240

Crystal structure of the T(6-4)C lesion in complex with a (6-4) DNA photolyase and repair of UV-induced (6-4) and Dewar photolesions.

A.F.Glas, S.Schneider, M.J.Maul, U.Hennecke, T.Carell.

ABSTRACT

UV-light irradiation induces the formation of highly mutagenic lesions in DNA, such as cis-syn cyclobutane pyrimidine dimers (CPD photoproducts), pyrimidine(6-4)pyrimidone photoproducts ((6-4) photoproducts) and their Dewar valence isomers ((Dew) photoproducts). Here we describe the synthesis of defined DNA strands containing these lesions by direct irradiation. We show that all lesions are efficiently repaired except for the T(Dew)T lesion, which cannot be cleaved by the repair enzyme under our conditions. A crystal structure of a T(6-4)C lesion containing DNA duplex in complex with the (6-4) photolyase from Drosophila melanogaster provides insight into the molecular recognition event of a cytosine derived photolesion for the first time. In light of the previously postulated repair mechanism, which involves rearrangement of the (6-4) lesions into strained four-membered ring repair intermediates, it is surprising that the not rearranged T(6-4)C lesion is observed in the active site. The structure, therefore, provides additional support for the newly postulated repair mechanism that avoids this rearrangement step and argues for a direct electron injection into the lesion as the first step of the repair reaction performed by (6-4) DNA photolyases.