ISDA

Deposition Date 2018-03-13

Release Date 2019-03-13

Last Version Date 2024-11-13

Entry Detail

PDB ID:

6CP9

Keywords:

TOXIN/ANTITOXIN

Title:

Contact-dependent growth inhibition toxin - immunity protein complex from Klebsiella pneumoniae 342

Biological Source:

Source Organism:

Klebsiella pneumoniae (strain 342) (Taxon ID: 507522)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.55 Å

R-Value Free:

0.23

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 21 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CdiA
Gene (Uniprot):KPK_4110
Chain IDs:A, C, E, G
Chain Length:126
Number of Molecules:4
Biological Source:Klebsiella pneumoniae (strain 342)

UniProt ID:B5Y0C2

Polymer Type:polypeptide(L)
Molecule:CdiI
Chain IDs:B, D, F, H
Chain Length:116
Number of Molecules:4
Biological Source:Klebsiella pneumoniae 342

Modified Residue

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

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.

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Primary Citation of related structures