5XM9

Crystal structure of AsfvPolX in complex with DNA enzyme.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.053 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of an RNA-cleaving DNAzyme.

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.

(2017) Nat Commun 8: 2006-2006

  • DOI: 10.1038/s41467-017-02203-x
  • Primary Citation of Related Structures:  5XM8, 5XMA

  • 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 me ...

    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.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Repair DNA polymerase X
A, B, C, D
177African swine fever virus (strain Badajoz 1971 Vero-adapted)EC: 2.7.7.7
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Go to UniProtKB:  P42494
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (36-MER)E,G36synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (23-mer)F,H23synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.053 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.940α = 90.00
b = 118.878β = 90.00
c = 235.955γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-13 
  • Released Date: 2018-01-24 
  • Deposition Author(s): Liu, H.H., Gan, J.H.

Funding OrganizationCountryGrant Number
Key Research and Development Project of ChinaChina2016YFA0500600

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release