5MCI

Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 11.9 MGy

Summary for 5MCI

• Entry DOI: 10.2210/pdb5mci/pdb
• Descriptor: Cellobiohydrolase CHBI, GLYCEROL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase, cellobiohydrolase, radiation damage, hydrolase
• Biological source: Daphnia pulex (Water flea)
• Total number of polymer chains: 2
• Total formula weight: 96832.68

Authors

Bury, C.S.,McGeehan, J.E.,Ebrahim, A.,Garman, E.F. (deposition date: 2016-11-09, release date: 2017-01-11, Last modification date: 2024-10-23)

Primary citation

Bury, C.S.,Carmichael, I.,Garman, E.F.
OH cleavage from tyrosine: debunking a myth.
J Synchrotron Radiat, 24:7-18, 2017

PubMed Abstract: During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.

PubMed: 28009542
DOI: 10.1107/S1600577516016775

Experimental method

X-RAY DIFFRACTION (2 Å)