1. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity
Mathew Stanley, Axel Knebel, Kay Hofmann, Nicola T Wood, Kuan-Chuan Pao, Ramasubramanian Sundaramoorthy, Satpal Virdee, Karim Rafie, Daan M F van Aalten, Peter D Mabbitt Nature . 2018 Apr;556(7701):381-385. doi: 10.1038/s41586-018-0026-1.
Ubiquitination is initiated by transfer of ubiquitin (Ub) from a ubiquitin-activating enzyme (E1) to a ubiquitin-conjugating enzyme (E2), producing a covalently linked intermediate (E2-Ub)1. Ubiquitin ligases (E3s) of the 'really interesting new gene' (RING) class recruit E2-Ub via their RING domain and then mediate direct transfer of ubiquitin to substrates2. By contrast, 'homologous to E6-AP carboxy terminus' (HECT) E3 ligases undergo a catalytic cysteine-dependent transthiolation reaction with E2-Ub, forming a covalent E3-Ub intermediate3,4. Additionally, RING-between-RING (RBR) E3 ligases have a canonical RING domain that is linked to an ancillary domain. This ancillary domain contains a catalytic cysteine that enables a hybrid RING-HECT mechanism5. Ubiquitination is typically considered a post-translational modification of lysine residues, as there are no known human E3 ligases with non-lysine activity. Here we perform activity-based protein profiling of HECT or RBR-like E3 ligases and identify the neuron-associated E3 ligase MYCBP2 (also known as PHR1) as the apparent single member of a class of RING-linked E3 ligase with esterification activity and intrinsic selectivity for threonine over serine. MYCBP2 contains two essential catalytic cysteine residues that relay ubiquitin to its substrate via thioester intermediates. Crystallographic characterization of this class of E3 ligase, which we designate RING-Cys-relay (RCR), provides insights into its mechanism and threonine selectivity. These findings implicate non-lysine ubiquitination in cellular regulation of higher eukaryotes and suggest that E3 enzymes have an unappreciated mechanistic diversity.
2. O-phospho-DL-threonine and O-phospho-L-threonine compared with their serine analogs
W Kwiatkowski, R H Blessing, W Maniukiewicz Acta Crystallogr C . 1996 Jul 15;52 ( Pt 7):1736-41. doi: 10.1107/s0108270195015708.
In crystals of O-phospho-DL-threonine and O-phospho-L-threonine, the molecules are zwitterions HO3-POCH-(CH3)CH(NH3+)CO2H linked by three-dimensional networks of strong P-O-H...O = P, C-O-H...O = P, N-H...O = P and N-H...O = C hydrogen bonds with (O...O) = 2.55 (3) A and (N...O) = 2.84 (4) A. Both the molecular conformations and the nearest-neighbor hydrogen-bonded surroundings are very similar in the racemic and enantiomeric crystals of the threonine compounds, but earlier studies of crystals of the analogous serine compounds have shown that the serine zwitterions HO3-POCH2CH(NH3+)CO2H have different conformations about the C beta-O gamma-P phosphate ester bonds and different hydrogen-bonded surroundings.
3. Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans
Toshihisa Ohshima, Haruhiko Sakuraba, Tomohiro Araki, Rina Nagano, Takuya Mikami, Kenji Fukui, Kazunari Yoneda Enzyme Microb Technol . 2020 Oct;140:109627. doi: 10.1016/j.enzmictec.2020.109627.
We report, for the first time, the three-dimensional structure and biochemical properties of a UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase (GalE-like L-ThrDH) from Phytophthora infestans, a plant disease-causing fungus. We identified GalE-like L-ThrDH using Kyoto Encyclopedia of Genes and Genomes (KEGG) database as a candidate target for the development of a new fungicide. The GalE-like L-ThrDH gene was expressed in Escherichia coli, and its product was purified and characterized. N-Acetylglycine was found to act as a competitive inhibitor of the enzyme (Ki =0.18 mM). The crystal structure of the unique hexameric GalE-like L-ThrDH was determined using the molecular replacement method at a resolution of 2.3 Å, in the presence of NAD+and citrate, an analogue of the substrate. Based on the molecular docking simulation, N-acetylglycine molecule was modeled into the active site and the binding mode and inhibition mechanism of N-acetylglycine were elucidated.