5YWR
Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
Summary for 5YWR
| Entry DOI | 10.2210/pdb5ywr/pdb |
| Descriptor | Ubiquitin-conjugating enzyme E2 N, E3 ubiquitin-protein ligase ZNRF1, TRIETHYLENE GLYCOL, ... (6 entities in total) |
| Functional Keywords | ubiquitin e3 ligase, znrf1, ubiquitin conjugating e2, ube2n, ubc13, signaling protein |
| Biological source | Homo sapiens (Human) More |
| Total number of polymer chains | 2 |
| Total formula weight | 27574.73 |
| Authors | Behera, A.P.,Naskar, P.,Datta, A.B. (deposition date: 2017-11-30, release date: 2018-06-06, Last modification date: 2024-03-27) |
| Primary citation | Behera, A.P.,Naskar, P.,Agarwal, S.,Banka, P.A.,Poddar, A.,Datta, A.B. Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications. Biochem. J., 475:1569-1582, 2018 Cited by PubMed Abstract: RING (eally nteresting ew ene) domains in ubiquitin RING E3 ligases exclusively engage ubiquitin (Ub)-loaded E2s to facilitate ubiquitination of their substrates. Despite such specificity, all RINGs characterized till date bind unloaded E2s with dissociation constants (s) in the micromolar to the sub-millimolar range. Here, we show that the RING domain of E3 ligase ZNRF1, an essential E3 ligase implicated in diverse cellular pathways, binds Ube2N with a of ∼50 nM. This high-affinity interaction is exclusive for Ube2N as ZNRF1 interacts with Ube2D2 with a of ∼1 µM, alike few other E3s. The crystal structure of ZNRF1 C-terminal domain in complex with Ube2N coupled with mutational analyses reveals the molecular basis of this unusual affinity. We further demonstrate that the ubiquitination efficiency of ZNRF1 : E2 pairs correlates with their affinity. Intriguingly, as a consequence of its high E2 affinity, an excess of ZNRF1 inhibits Ube2N-mediated ubiquitination at concentrations ≥500 nM instead of showing enhanced ubiquitination. This suggests a novel mode of activity regulation of E3 ligases and emphasizes the importance of E3-E2 balance for the optimum activity. Based on our results, we propose that overexpression-based functional analyses on E3 ligases such as ZNRF1 must be approached with caution as enhanced cellular levels might result in aberrant modification activity. PubMed: 29626159DOI: 10.1042/BCJ20170909 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.47 Å) |
Structure validation
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