Our studies of the ubiquitin-ligase E3, called gp78, are conducted in collaboration with Drs. Allan Weissman and Xinhua Ji, CCR. The gp78 protein has a role in sarcoma metastasis, and it is an excellent target for a combined structural and molecular biological investigation of mechanism and intervention. We have reported major findings from this project in a series of four publications. The effort is an interdisciplinary effort involving molecular biology in the Weissman lab, NMR structural biology and biophysics in the Byrd lab, and X-ray crystallograpny in the Ji lab. These studies uncovered a new aspect of the E2:E3 interaction, wherein the action of a newly identified E2-binding site in gp78 results in an allosteric effect on the E2 Ube2g2 increasing the affinity for the gp78-RING finger domain by 50-fold. We also showed that the effect of the binding region (G2BR) is effective for other RING finger containing E3s. The generalization of this phenomenon is leading to a broader understanding of ubiquitination and shifting in the paradigm for the molecular mechanism of ubiquitin transfer. These studies have been extended in both the Weissman and Byrd labs. We published new structural information on the ternary complex of the gp78-RING:Ube2g2:G2BR system from both NMR and crystallographic studies (EMBO J), and a related approach was undertaken for a different E2:E3 pair and published in Molecular Cell. We have examined the solution structure of the CUE domain, which is a distinct functional domain within gp78, and its interactions with ubiquitin and di-ubiquitin. These results were published in Structure. We are continuing our examination of the detailed interactions and mechanism of ubiquitin transfer. Another aspect of this system is the role of dynamics in determining chain linking specificity. We are employing NMR methods to directly correlate molecular motions/dynamics of regions of the Ube2g2 enzyme with the pertinent interactions to domains of gp78. These data will be critical to developing an overview of the reaction cycle for ubiquitin loading, transfer, and chain specificity. We have added the use of small-angle X-ray scattering (SAXS), conducted on protein complexes in solution, to enable us to examine larger constructs of the ubiquitination machinery. These efforts will continue for the next year.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Investigator-Initiated Intramural Research Projects (ZIA)
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National Cancer Institute Division of Basic Sciences
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Chakrabarti, Kalyan S; Li, Jess; Das, Ranabir et al. (2017) Conformational Dynamics and Allostery in E2:E3 Interactions Drive Ubiquitination: gp78 and Ube2g2. Structure 25:794-805.e5
Gill, Michelle L; Byrd, R Andrew (2014) Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism. Nat Struct Mol Biol 21:1022-3
Huang, Tao; Li, Jess; Byrd, R Andrew (2014) Solution structure of lysine-free (K0) ubiquitin. Protein Sci 23:662-7
Das, Ranabir; Liang, Yu-He; Mariano, Jennifer et al. (2013) Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J 32:2504-16
Byrd, R Andrew; Weissman, Allan M (2013) Compact Parkin only: insights into the structure of an autoinhibited ubiquitin ligase. EMBO J 32:2087-9
Metzger, Meredith B; Liang, Yu-He; Das, Ranabir et al. (2013) A structurally unique E2-binding domain activates ubiquitination by the ERAD E2, Ubc7p, through multiple mechanisms. Mol Cell 50:516-27
Liu, Shan; Chen, Yinghua; Li, Jess et al. (2012) Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains. Structure 20:2138-50