5XM9

Crystal structure of AsfvPolX in complex with DNA enzyme.

Summary for 5XM9

• Entry DOI: 10.2210/pdb5xm9/pdb
• Descriptor: Repair DNA polymerase X, DNA (36-MER), DNA (23-mer) (3 entities in total)
• Functional Keywords: polx, dna enzyme, complex, transferase-dna complex, transferase/dna
• Biological source: African swine fever virus (strain Badajoz 1971 Vero-adapted) (Ba71V); More
• Total number of polymer chains: 8
• Total formula weight: 118574.16

Authors

Liu, H.H.,Gan, J.H. (deposition date: 2017-05-13, release date: 2018-01-24, Last modification date: 2023-11-22)

Primary citation

Liu, H.,Yu, X.,Chen, Y.,Zhang, J.,Wu, B.,Zheng, L.,Haruehanroengra, P.,Wang, R.,Li, S.,Lin, J.,Li, J.,Sheng, J.,Huang, Z.,Ma, J.,Gan, J.
Crystal structure of an RNA-cleaving DNAzyme.
Nat Commun, 8:2006-2006, 2017

PubMed Abstract: In addition to storage of genetic information, DNA can also catalyze various reactions. RNA-cleaving DNAzymes are the catalytic DNAs discovered the earliest, and they can cleave RNAs in a sequence-specific manner. Owing to their great potential in medical therapeutics, virus control, and gene silencing for disease treatments, RNA-cleaving DNAzymes have been extensively studied; however, the mechanistic understandings of their substrate recognition and catalysis remain elusive. Here, we report three catalytic form 8-17 DNAzyme crystal structures. 8-17 DNAzyme adopts a V-shape fold, and the Pb cofactor is bound at the pre-organized pocket. The structures with Pb and the modification at the cleavage site captured the pre-catalytic state of the RNA cleavage reaction, illustrating the unexpected Pb-accelerated catalysis, intrinsic tertiary interactions, and molecular kink at the active site. Our studies reveal that DNA is capable of forming a compacted structure and that the functionality-limited bio-polymer can have a novel solution for a functional need in catalysis.

PubMed: 29222499
DOI: 10.1038/s41467-017-02203-x

Experimental method

X-RAY DIFFRACTION (3.053 Å)