5XMA image
Entry Detail
PDB ID:
5XMA
Keywords:
Title:
Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group
Biological Source:
PDB Version:
Deposition Date:
2017-05-13
Release Date:
2018-01-24
Method Details:
Experimental Method:
Resolution:
3.80 Å
R-Value Free:
0.28
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Repair DNA polymerase X
Chain IDs:A, B
Chain Length:177
Number of Molecules:2
Biological Source:African swine fever virus (strain Badajoz 1971 Vero-adapted)
Polymer Type:polydeoxyribonucleotide
Description:DNA (36-MER)
Chain IDs:C (auth: E)
Chain Length:36
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Description:DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3')
Chain IDs:D (auth: F)
Chain Length:23
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
Crystal structure of an RNA-cleaving DNAzyme.
Nat Commun 8 2006 2006 (2017)
PMID: 29222499 DOI: 10.1038/s41467-017-02203-x

Abstact

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 Pb2+ cofactor is bound at the pre-organized pocket. The structures with Pb2+ and the modification at the cleavage site captured the pre-catalytic state of the RNA cleavage reaction, illustrating the unexpected Pb2+-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.

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Primary Citation of related structures