9EMK
DupA from legionella covalently bound to ubiquitin-based probe
This is a non-PDB format compatible entry.
Summary for 9EMK
| Entry DOI | 10.2210/pdb9emk/pdb |
| Descriptor | Septation initiation protein, Polyubiquitin-B, [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate, ... (4 entities in total) |
| Functional Keywords | covalent complex, chemical warhead, ubiquitin enzyme, infection, unknown function |
| Biological source | Legionella pneumophila subsp. pneumophila More |
| Total number of polymer chains | 6 |
| Total formula weight | 144979.89 |
| Authors | Kim, R.Q.,Kloet, M.S.,van der Heden van Noort, G. (deposition date: 2024-03-08, release date: 2024-10-16) |
| Primary citation | Kloet, M.S.,Mukhopadhyay, R.,Mukherjee, R.,Misra, M.,Jeong, M.,Talavera Ormeno, C.M.P.,Moutsiopoulou, A.,Tjokrodirijo, R.T.N.,van Veelen, P.A.,Shin, D.,Dikic, I.,Sapmaz, A.,Kim, R.Q.,van der Heden van Noort, G.J. Covalent Probes To Capture Legionella pneumophila Dup Effector Enzymes. J.Am.Chem.Soc., 146:26957-26964, 2024 Cited by PubMed Abstract: Upon infection of host cells, releases a multitude of effector enzymes into the cell's cytoplasm that hijack a plethora of cellular activities, including the host ubiquitination pathways. Effectors belonging to the SidE-family are involved in noncanonical serine phosphoribosyl ubiquitination of host substrate proteins contributing to the formation of a Legionella-containing vacuole that is crucial in the onset of Legionnaires' disease. This dynamic process is reversed by effectors called Dups that hydrolyze the phosphodiester in the phosphoribosyl ubiquitinated protein. We installed reactive warheads on chemically prepared ribosylated ubiquitin to generate a set of probes targeting these Legionella enzymes. In vitro tests on recombinant DupA revealed that a vinyl sulfonate warhead was most efficient in covalent complex formation. Mutagenesis and X-ray crystallography approaches were used to identify the site of covalent cross-linking to be an allosteric cysteine residue. The subsequent application of this probe highlights the potential to selectively enrich the Dup enzymes from Legionella-infected cell lysates. PubMed: 39288007DOI: 10.1021/jacs.4c08168 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.17 Å) |
Structure validation
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