PDBsum entry 6imk

Ligase/DNA

PDB id: 6imk

Contents

Protein chain

409 a.a.

DNA/RNA

Waters ×100

PDB id:

6imk

Name:

Ligase/DNA

Title:

The crystal structure of asfvlig:cg complex

Structure:

DNA ligase. Chain: a. Synonym: np419l,pnp419l. Engineered: yes. 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'). Chain: c. Engineered: yes.

Source:

African swine fever virus. Asfv. Organism_taxid: 10497. Gene: np419l. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.50Å R-factor: 0.208 R-free: 0.254

Authors:

Y.Q.Chen,J.H.Gan

Key ref:

Y.Chen et al. (2019). Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues. Nat Commun, 10, 387. PubMed id: 30674878 DOI: 10.1038/s41467-019-08296-w

Date:

23-Oct-18 Release date: 27-Feb-19

Protein chain

P35970  (DNLI_ASFB7) -  DNA ligase from African swine fever virus (strain Badajoz 1971 Vero-adapted)

Seq: 419 a.a.

Struc: 409 a.a.

DNA/RNA chains

C-C-A-G-T-C-C-G-A-C-C-C-G-C-A-T-C-C-C-G-G-A 22 bases

T-C-C-G-G-G-A-T-G-C-G-G 12 bases

G-T-C-G-G-A-C-T-G-G 10 bases

Enzyme reactions

• Enzyme class: E.C.6.5.1.1 - Dna ligase (ATP).
• Reaction: ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41467-019-08296-w

Nat Commun 10:387 (2019)

PubMed id: 30674878

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

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

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.