6ITW

Crystal structure of Atu4351 from Agrobacterium tumefaciens

Summary for 6ITW

• Entry DOI: 10.2210/pdb6itw/pdb
• Descriptor: Type VI immunity protein Atu4351 (2 entities in total)
• Functional Keywords: type six secretion system;effector-immunity pair; tdi1; gad-like domain; duf1851 domain, antitoxin
• Biological source: Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
• Total number of polymer chains: 1
• Total formula weight: 26357.35

Authors

Shi, L.,Gao, Z.,Zhang, H.,Dong, Y. (deposition date: 2018-11-26, release date: 2019-03-20, Last modification date: 2024-10-16)

Primary citation

Shi, L.,Gao, Z.,Zhang, T.,Zhang, H.,Dong, Y.
Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens.
Acta Crystallogr F Struct Biol Commun, 75:153-158, 2019

PubMed Abstract: The type VI secretion system (T6SS) is a novel multiprotein needle-like apparatus that is distributed widely in Gram-negative bacteria. Bacteria harboring T6SSs inject various effectors into both eukaryotic and prokaryotic cells for interspecies competition or virulence-related processes. The toxicities of the effectors can be neutralized by their cognate immunity proteins. Tde1 (Atu4350)-Tdi1 (Atu4351) has recently been characterized as a T6SS effector-immunity pair in the soil bacterium Agrobacterium tumefaciens and the neutralization mechanism remains unknown. Here, the crystal structure of the immunity protein Tdi1 was determined at 2.40 Å resolution by the single-wavelength anomalous dispersion method. Structural analysis suggested that it is composed of a GAD-like domain and an inserted DUF1851 domain, and both domains show low structural similarities to known structures. There is a positive groove mainly located in the GAD-like domain that may be associated with nucleotide binding. The structure provides a basis for further study of the positive groove as a potential active site.

PubMed: 30839288
DOI: 10.1107/S2053230X19000815

Experimental method

X-RAY DIFFRACTION (2.4 Å)