ISDA

Entry Detail

PDB ID:

6CP8

Keywords:

TOXIN/ANTITOXIN

Title:

Contact-dependent growth inhibition toxin-immunity protein complex from from E. coli 3006

Biological Source:

Source Organism:

Escherichia coli

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2018-03-13

Release Date:

2019-03-13

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.21

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:CdiA
Mutations:deltaN332
Chain IDs:A, B
Chain Length:163
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:A0A2A2CAY5

Protein Blast

Polymer Type:polypeptide(L)
Description:CdiI
Chain IDs:C, D
Chain Length:164
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:A0A2A2C800

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MSE	A	MET	modified residue

Ligand Molecules

EPE

GOL

Primary Citation

Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins.

Gucinski, G.C, Michalska, K, Garza-Sanchez, F, Eschenfeldt, W.H, Stols, L, Nguyen, J.Y, Goulding, C.W, Joachimiak, A, Hayes, C.S, Lepore, R, Kryshtafovych, A, Alahuhta, M, Veraszto, H.A, Bomble, Y.J, Bufton, J.C, Bullock, A.N, Caba, C, Cao, H, Davies, O.R, Desfosses, A, Dunne, M, Fidelis, K, Goulding, C.W, Gurusaran, M, Gutsche, I, Harding, C.J, Hartmann, M.D, Hayes, C.S, Joachimiak, A, Leiman, P.G, Loppnau, P, Lovering, A.L, Lunin, V.V, Michalska, K, Mir-Sanchis, I, Mitra, A, Moult, J, Phillips Jr, G.N, Pinkas, D.M, Rice, P.A, Tong, Y, Topf, M, Walton, J.D, Schwede, T.Show

Structure 27 1660 ? (2019)

PMID: 31515004 DOI: 10.1016/j.str.2019.08.010

Abstact

Contact-dependent growth inhibition (CDI) is a form of interbacterial competition mediated by CdiB-CdiA two-partner secretion systems. CdiA effector proteins carry polymorphic C-terminal toxin domains (CdiA-CT), which are neutralized by specific CdiI immunity proteins to prevent self-inhibition. Here, we present the crystal structures of CdiA-CT⋅CdiI complexes from Klebsiella pneumoniae 342 and Escherichia coli 3006. The toxins adopt related folds that resemble the ribonuclease domain of colicin D, and both are isoacceptor-specific tRNases that cleave the acceptor stem of deacylated tRNAGAUIle. Although the toxins are similar in structure and substrate specificity, CdiA-CTKp342 activity requires translation factors EF-Tu and EF-Ts, whereas CdiA-CTEC3006 is intrinsically active. Furthermore, the corresponding immunity proteins are unrelated in sequence and structure. CdiIKp342 forms a dimeric β sandwich, whereas CdiIEC3006 is an α-solenoid monomer. Given that toxin-immunity genes co-evolve as linked pairs, these observations suggest that the similarities in toxin structure and activity reflect functional convergence.

Legend

Protein

Chemical

Disease

Primary Citation of related structures