7cpw

From Proteopedia

Complex structure of DNA with self-catalyzed depurination activity

PDB ID 7cpw

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Structural highlights

7cpw is a 4 chain structure with sequence from African swine fever virus and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.849Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPOLX_ASFB7 Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.^[1] ^[2]

Publication Abstract from PubMed

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.

Crystallization and Structural Determination of 8-17 DNAzyme.,Liu H, Mao S, Sheng J, Gan J Methods Mol Biol. 2022;2439:117-130. doi: 10.1007/978-1-0716-2047-2_9. PMID:35226319^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Garcia-Escudero R, Garcia-Diaz M, Salas ML, Blanco L, Salas J. DNA polymerase X of African swine fever virus: insertion fidelity on gapped DNA substrates and AP lyase activity support a role in base excision repair of viral DNA. J Mol Biol. 2003 Mar 7;326(5):1403-12. PMID:12595253
↑ Showalter AK, Byeon IJ, Su MI, Tsai MD. Solution structure of a viral DNA polymerase X and evidence for a mutagenic function. Nat Struct Biol. 2001 Nov;8(11):942-6. PMID:11685239 doi:10.1038/nsb1101-942
↑ Liu H, Mao S, Sheng J, Gan J. Crystallization and Structural Determination of 8-17 DNAzyme. Methods Mol Biol. 2022;2439:117-130. PMID:35226319 doi:10.1007/978-1-0716-2047-2_9