7MFR

Crystal Structure of a Fab fragment bound to peptide GGM

Summary for 7MFR

• Entry DOI: 10.2210/pdb7mfr/pdb
• Descriptor: Antibody fragment - Light Chain of fab, Antibody fragment - Heavy Chain of fab, GLY-GLY-MET, ... (5 entities in total)
• Functional Keywords: deubiquitinase ubiquitin n-terminal ubiquitination antibody tools ube2w anti-ggx, immune system
• Biological source: Oryctolagus cuniculus; More
• Total number of polymer chains: 6
• Total formula weight: 94377.10

Authors

Sudhamsu, J. (deposition date: 2021-04-10, release date: 2021-06-16, Last modification date: 2024-10-23)

Primary citation

Davies, C.W.,Vidal, S.E.,Phu, L.,Sudhamsu, J.,Hinkle, T.B.,Chan Rosenberg, S.,Schumacher, F.R.,Zeng, Y.J.,Schwerdtfeger, C.,Peterson, A.S.,Lill, J.R.,Rose, C.M.,Shaw, A.S.,Wertz, I.E.,Kirkpatrick, D.S.,Koerber, J.T.
Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W.
Nat Commun, 12:4608-4608, 2021

PubMed Abstract: The ubiquitin conjugating enzyme UBE2W catalyzes non-canonical ubiquitination on the N-termini of proteins, although its substrate repertoire remains unclear. To identify endogenous N-terminally-ubiquitinated substrates, we discover four monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. We solve the structure of one such antibody bound to a Gly-Gly-Met peptide to reveal the molecular basis for its selective recognition. We use these antibodies in conjunction with mass spectrometry proteomics to map N-terminal ubiquitination sites on endogenous substrates of UBE2W. These substrates include UCHL1 and UCHL5, where N-terminal ubiquitination distinctly alters deubiquitinase (DUB) activity. This work describes an antibody toolkit for enrichment and global profiling of endogenous N-terminal ubiquitination sites, while revealing functionally relevant substrates of UBE2W.

PubMed: 34326324
DOI: 10.1038/s41467-021-24669-6

Experimental method

X-RAY DIFFRACTION (2.848 Å)