7CPW

Complex structure of DNA with self-catalyzed depurination activity

Summary for 7CPW

• Entry DOI: 10.2210/pdb7cpw/pdb
• Descriptor: DNA polymerase beta-like protein, DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3') (3 entities in total)
• Functional Keywords: dnazyme, depurination, gaga motif, dna, transferase-dna complex, transferase/dna
• Biological source: African swine fever virus (ASFV); More
• Total number of polymer chains: 4
• Total formula weight: 53587.45

Authors

Gan, J.H. (deposition date: 2020-08-08, release date: 2021-08-18, Last modification date: 2023-11-29)

Primary citation

Liu, H.,Mao, S.,Sheng, J.,Gan, J.
Crystallization and Structural Determination of 8-17 DNAzyme.
Methods Mol.Biol., 2439:117-130, 2022

PubMed Abstract: DNAzymes are a group of DNA molecules that can catalyze various chemical reactions. Owing to their great application potentials, DNAzymes have received significant attention. However, due to their intrinsic difficulties in crystallization and structural determination, only very limited structural information of DNAzymes is available to date. Using co-crystallization with the African Swine Fever Virus Polymerase X (AsfvPolX) protein, we have recently solved a complex structure of the 8-17 DNAzyme, which represents the first structure of the catalytically active RNA-cleaving DNAzyme. In this chapter, we describe the detailed protocols including gene construction, AsfvPolX expression and purification, crystallization, structure determination, and in vitro cleavage assay. While the specific methods described herein were originally designed for the 8-17 DNAzyme, they can also be utilized to solve other DNAzyme structures.

PubMed: 35226319
DOI: 10.1007/978-1-0716-2047-2_9

Experimental method

X-RAY DIFFRACTION (2.849 Å)