5WFY

Crystal structure of DNA-binding domain of the bacteriophage T4 ligase

Summary for 5WFY

• Entry DOI: 10.2210/pdb5wfy/pdb
• Descriptor: DNA ligase, GLYCEROL (3 entities in total)
• Functional Keywords: ligase-dna complex, ligase
• Biological source: Enterobacteria phage T4
• Total number of polymer chains: 1
• Total formula weight: 15949.74

Authors

Shi, K.,Aihara, H. (deposition date: 2017-07-13, release date: 2018-09-26, Last modification date: 2024-10-23)

Primary citation

Shi, K.,Bohl, T.E.,Park, J.,Zasada, A.,Malik, S.,Banerjee, S.,Tran, V.,Li, N.,Yin, Z.,Kurniawan, F.,Orellana, K.,Aihara, H.
T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46:10474-10488, 2018

PubMed Abstract: DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.

PubMed: 30169742
DOI: 10.1093/nar/gky776

Experimental method

X-RAY DIFFRACTION (1.4 Å)