1IQR

Crystal structure of DNA photolyase from Thermus thermophilus

Summary for 1IQR

• Entry DOI: 10.2210/pdb1iqr/pdb
• Descriptor: photolyase, PHOSPHATE ION, FLAVIN-ADENINE DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: dna repair, cyclobutane pyrimidine dimer (cpd), fad, photoreactivating enzyme, dna-binding, riken structural genomics/proteomics initiative, rsgi, structural genomics, lyase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 48854.46

Authors

Komori, H.,Masui, R.,Kuramitsu, S.,Yokoyama, S.,Shibata, T.,Inoue, Y.,Miki, K.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2001-07-27, release date: 2001-11-28, Last modification date: 2023-12-27)

Primary citation

Komori, H.,Masui, R.,Kuramitsu, S.,Yokoyama, S.,Shibata, T.,Inoue, Y.,Miki, K.
Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.
Proc.Natl.Acad.Sci.USA, 98:13560-13565, 2001

PubMed Abstract: DNA photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. The other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. Photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. The native structures of both types of photolyases have already been determined, but the mechanism of substrate recognition remains largely unclear because of the lack of structural information regarding the photolyase-substrate complex. Photolyase from Thermus thermophilus, the first thermostable class I photolyase found, is favorable for function analysis, but even the type of the second cofactor has not been identified. Here, we report the crystal structures of T. thermophilus photolyase in both forms of the native enzyme and the complex along with a part of its substrate, thymine. A structural comparison with other photolyases suggests that T. thermophilus photolyase has structural features allowing for thermostability and that its light-harvesting cofactor binding site bears a close resemblance to a deazaflavin-type photolyase. One thymine base is found at the hole, a putative substrate-binding site near the catalytic cofactor in the complex form. This structural data for the photolyase-thymine complex allow us to propose a detailed model for the pyrimidine-dimer recognition mechanism.

PubMed: 11707580
DOI: 10.1073/pnas.241371398

Experimental method

X-RAY DIFFRACTION (2.1 Å)