Hijacking the host ubiquitin pathway: structural strategies of bacterial E3 ubiquitin ligases

Abstract

Ubiquitinylation of proteins is a critical mechanism in regulating numerous eukaryotic cellular processes including cell cycle progression, inflammatory response, and vesicular trafficking. Given the importance of ubiquitinylation, it is not surprising that several pathogenic bacteria have developed strategies to exploit various stages of the ubiquitin pathway for their own benefit. One such strategy is the delivery of bacterial 'effector' proteins into the host cell cytosol, which mimic the activities of components of the host ubiquitin pathway. Recent studies have highlighted a number of bacterial effectors that functionally mimic the activity of eukaryotic E3 ubiquitin ligases, including a novel structural class of bacterial E3 ligases that provides a striking example of convergent evolution.

Figure 1

Bacterial mimics of eukaryotic RING/U-box E3 ligases. (A). Using the Phyre threading program, the sequence of U-box1 of L. pneumophila LubX was aligned to known structures and the structure was modeled to its best fit, human E3 traf6 (E-value of 2.6e⁻¹¹; estimated precision of 100%); the RING/U-box structure of H. sapien, Rbx-1 (PDB ID 3DPL); the core fold of P. syringae, AvrPtoB (PDB ID 2FD4). (B) Visualization of the E2-binding site residues of Rbx-1 with homologous regions in LubX and AvrPtoB. The three putative E2-binding residues are shown.

Figure 2

SopA is a HECT-like E3 ligase. (A) Overall structure of SopA_163–782 (PDB ID 2QYU); the HECT domain of SopA is shown in blue and the N-terminal β-helix domain in yellow. The catalytic cysteine is signified in red. N, NH2 terminus; C, COOH terminus. (B) Schematic diagram of the transfer of ubiquitin. Ubiquitin is shown in red. The C lobe of a generic HECT E3 or SopA is positioned similarly to accept ubiquitin following binding of Ub-charged E2 (green). However, the placement of the substrate binding (SBD; yellow) domain of SopA on the opposite end of the N lobe as found in eukaryotic HECT E3s likely requires a significantly different conformational change to facilitate ubiquitin transfer to a target substrate (grey box).

Figure 3

NEL family of E3 ligases. (A) The structure of SspH2_166–783 (PBD ID 3G06), IpaH1.4_265–575 (PDB ID 3CKD), and Ipa3_25–561 (PDB ID 3CVR) is shown with leucine-rich repeat (LRR) domain in blue and the novel E3 ligase (NEL) domain in green. The catalytic cysteine residue is shown in red. N, NH2 terminus; C, COOH terminus. (B) Conformational changes likely activate the NEL family of E3 ligases. The structures of Shigella IpaH3 and Salmonella SspH2 suggests a dramatic hinge motion as the NEL domain rotates 180° from the closed conformation indicated by the structure of SspH2 to the open position represented by the IpaH3 structure. The catalytic cysteine residue is shown in red. N, NH2 terminus; C, COOH terminus.