PDBsum entry 4v3k

Ligase

PDB id: 4v3k

Contents

Protein chains

146 a.a.

77 a.a.

75 a.a.

70 a.a.

Ligands

EDO ×5

Metals

_ZN ×4

_CL ×6

Waters ×368

References listed in PDB file

Key reference

• Title: Activation of a primed ring e3-E2-Ubiquitin complex by non-Covalent ubiquitin.
• Authors: L.Buetow, M.Gabrielsen, N.G.Anthony, H.Dou, A.Patel, H.Aitkenhead, G.J.Sibbet, B.O.Smith, D.T.Huang.
• Ref.: Mol Cell, 2015, 58, 297-310. [DOI no: 10.1016/j.molcel.2015.02.017]
• PubMed id: 25801170

Abstract

RING ubiquitin ligases (E3) recruit ubiquitin-conjugate enzymes (E2) charged with ubiquitin (Ub) to catalyze ubiquitination. Non-covalent Ub binding to the backside of certain E2s promotes processive polyUb formation, but the mechanism remains elusive. Here, we show that backside bound Ub (Ub(B)) enhances both RING-independent and RING-dependent UbcH5B-catalyzed donor Ub (Ub(D)) transfer, but with a more prominent effect in RING-dependent transfer. Ub(B) enhances RING E3s' affinities for UbcH5B-Ub, and RING E3-UbcH5B-Ub complex improves Ub(B)'s affinity for UbcH5B. A comparison of the crystal structures of a RING E3, RNF38, bound to UbcH5B-Ub in the absence and presence of Ub(B), together with molecular dynamics simulation and biochemical analyses, suggests Ub(B) restricts the flexibility of UbcH5B's α1 and α1β1 loop. Ub(B) supports E3 function by stabilizing the RING E3-UbcH5B-Ub complex, thereby improving the catalytic efficiency of Ub transfer. Thus, Ub(B) serves as an allosteric activator of RING E3-mediated Ub transfer.