3QHT

Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO

Summary for 3QHT

• Entry DOI: 10.2210/pdb3qht/pdb
• Descriptor: Ubiquitin-like protein SMT3, Monobody ySMB-1, GLYCEROL, ... (4 entities in total)
• Functional Keywords: fibronectin type iii, yeast small ubiquitin-like modifier, smt3, de novo protein
• Biological source: Saccharomyces cerevisiae (yeast); More
• Total number of polymer chains: 4
• Total formula weight: 43934.25

Authors

Koide, S.,Gilbreth, R.N. (deposition date: 2011-01-26, release date: 2011-05-11, Last modification date: 2023-09-13)

Primary citation

Gilbreth, R.N.,Truong, K.,Madu, I.,Koide, A.,Wojcik, J.B.,Li, N.S.,Piccirilli, J.A.,Chen, Y.,Koide, S.
Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.
Proc.Natl.Acad.Sci.USA, 108:7751-7756, 2011

PubMed Abstract: Discriminating closely related molecules remains a major challenge in the engineering of binding proteins and inhibitors. Here we report the development of highly selective inhibitors of small ubiquitin-related modifier (SUMO) family proteins. SUMOylation is involved in the regulation of diverse cellular processes. Functional differences between two major SUMO isoforms in humans, SUMO1 and SUMO2/3, are thought to arise from distinct interactions mediated by each isoform with other proteins containing SUMO-interacting motifs (SIMs). However, the roles of such isoform-specific interactions are largely uncharacterized due in part to the difficulty in generating high-affinity, isoform-specific inhibitors of SUMO/SIM interactions. We first determined the crystal structure of a "monobody," a designed binding protein based on the fibronectin type III scaffold, bound to the yeast homolog of SUMO. This structure illustrated a mechanism by which monobodies bind to the highly conserved SIM-binding site while discriminating individual SUMO isoforms. Based on this structure, we designed a SUMO-targeted library from which we obtained monobodies that bound to the SIM-binding site of human SUMO1 with K(d) values of approximately 100 nM but bound to SUMO2 400 times more weakly. The monobodies inhibited SUMO1/SIM interactions and, unexpectedly, also inhibited SUMO1 conjugation. These high-affinity and isoform-specific inhibitors will enhance mechanistic and cellular investigations of SUMO biology.

PubMed: 21518904
DOI: 10.1073/pnas.1102294108

Experimental method

X-RAY DIFFRACTION (2.4 Å)