5XMA

Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

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, 5XM9, 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 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 ...

    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 2+ cofactor is bound at the pre-organized pocket. The structures with Pb 2+ and the modification at the cleavage site captured the pre-catalytic state of the RNA cleavage reaction, illustrating the unexpected Pb 2+ -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. ganjhh@fudan.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Repair DNA polymerase XA, B177African swine fever virus BA71VMutation(s): 0 
Gene Names: Ba71V-97O174L
EC: 2.7.7.7
UniProt
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore P42494 
Go to UniProtKB:  P42494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42494
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (36-MER)C [auth E]36synthetic construct
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
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')D [auth F]23synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.846α = 90
b = 78.846β = 90
c = 241.677γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




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 OrganizationLocationGrant Number
Key Research and Development Project of ChinaChina2016YFA0500600

Revision History  (Full details and data files)

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