Journal:Acta Cryst F:S2053230X19000815

Crystal structure of Type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens

Lingling Shi, Zengqiang Gao, Tianyi Zhang, Heng Zhang and Yuhui Dong ^[1]

Molecular Tour
Structure of Type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens is composed a GAD-like domain inserted by a DUF1851 domain, and such domain organization is rare in known structures. There is a positive groove that is mainly located in the GAD-like domain that may be associated with nucleotide-binding.

(PDB ID 6itw). The GAD-like domain and the DUF1851 domain are shown in orange and cyan, respectively. The GAD-like domain structure is composed a seven-stranded twisted antiparallel β-sheet (β1↑-β2↓-β3↑-β4↓-β5↑-β6↓-β7↑) in the N-terminus and a two-stranded antiparallel β-sheet (β10↓-β11↑) in the C-terminus, surrounded by six helices (α1-α5 and η1). The DUF1851 domain is composed of a two-stranded antiparallel β-sheet (β8↓-β9↑) and four helices (η2-η3 and α6-α7). Therefore, the DUF1851 domain probably exists as an insertion of the GAD-like domain rather than an independent domain.

(blue, positive; red, negative), colored by its local electrostatic potential. Remarkably, there is a groove that is mainly composed of β7, η1 and α5 in the GAD-like domain and extends to β8 in theDUF1851 domain. Many of the residues constituting the groove are conserved or highly conserved among Tdi1 homologs. Inspection of the surface charge distribution of the groove revealed it is covered with dominantly positive charges, which may be associated with nucleotide-binding.

The GAD domain exists as an insertion in bacterial aminoacyl-tRNA synthetases (aaRSs), such as aspartyl- and glutamyl-tRNA synthetases (AspRS and GluRS). Structural comparison of Tdi1 with the GAD domain of E. coli AspRS (PDB ID 1c0a) showed they have similar topology structures (with a RMSD of 3.9). (PDB ID 1c0a, in gray) shown as cartoon. An AMP molecule (shown as green sticks) is bound in E. coli AspRS.

(only the AMP molecule is shown). An AMP molecule (shown in green spacefill representation) is bound in E. coli AspRS. The AMP is buried in Tdi1 and far from its positive groove, indicating Tdi1 may have a different active site from AspRS.

PDB reference: Atu4351 from Agrobacterium tumefaciens, 6itw.

References

1. ↑ 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. 2019 Mar 1;75(Pt 3):153-158. doi:, 10.1107/S2053230X19000815. Epub 2019 Feb 20. PMID:30839288 doi:http://dx.doi.org/10.1107/S2053230X19000815