6IML

The crystal structure of AsfvLIG:CT1 complex

• PDB DOI:  https://doi.org/10.2210/pdb6IML/pdb
• NAKB: 6IML

• Classification: LIGASE/DNA
• Organism(s): African swine fever virus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-23 Released: 2019-02-27 
• Deposition Author(s): Chen, Y.Q., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.268 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 

Literature

Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues.

Chen, Y., Liu, H., Yang, C., Gao, Y., Yu, X., Chen, X., Cui, R., Zheng, L., Li, S., Li, X., Ma, J., Huang, Z., Li, J., Gan, J.

(2019) Nat Commun 10: 387-387

• PubMed: 30674878 
• DOI: https://doi.org/10.1038/s41467-019-08296-w
• Primary Citation of Related Structures:  
  6IMJ, 6IMK, 6IML, 6IMN


• PubMed Abstract: 
  

African swine fever virus (ASFV) is contagious and can cause highly lethal disease in pigs. ASFV DNA ligase (AsfvLIG) is one of the most error-prone ligases identified to date; it catalyzes DNA joining reaction during DNA repair process of ASFV and plays important roles in mutagenesis of the viral genome. Here, we report four AsfvLIG:DNA complex structures and demonstrate that AsfvLIG has a unique N-terminal domain (NTD) that plays critical roles in substrate binding and catalytic complex assembly. In combination with mutagenesis, in vitro binding and catalytic assays, our study reveals that four unique active site residues (Asn153 and Leu211 of the AD domain; Leu402 and Gln403 of the OB domain) are crucial for the catalytic efficiency of AsfvLIG. These unique structural features can serve as potential targets for small molecule design, which could impair genome repair in ASFV and help combat this virus in the future.

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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, 200433, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.67 kDa 
• Atom Count: 4,102 
• Modelled Residue Count: 447 
• Deposited Residue Count: 463 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	419	African swine fever virus	Mutation(s): 0  Gene Names: NP419L EC: 6.5.1.1
UniProt
Find proteins for P35970 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore P35970  Go to UniProtKB:  P35970

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')	B [auth C]	22	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*T)-3')	C [auth D]	12	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')	D [auth E]	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.268 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.244	α = 90
b = 53.735	β = 100.47
c = 76.232	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Chen, Y.Q., Gan, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370728

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release