Linear specific OTU-type DUB SnOTU from the pathogen S. negenvensis in complex with linear di-ubiquitin

Functional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis.

PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)

In the crystal structure there is domain swapping likely occurring. The two ubiquitin units of chains B or D are spread over two DUB molecules (A or C). A biological assembly, for example, would more likely be Chain A/Chain B:77-152 linked via peptide bond from B152 to D1 to chain D, residues 1-76.

cDNA FLJ51326,highly similar to Homo sapiens ubiquitin B (UBB),mRNA

MSLPVKERPDAIYTFEGKTYENTSFSKTGIPIVGQPLKMEAYVHKEYTHVTSLEGKRFKSQLEEAAKIYGEQLHEIQGDG
NALTTAFATSFLYLLNGNATLIATFDNILIGLDAHKNIPPVRQTIEKLKVKNDLELKQILASNETMFAFSSVIRHLARQK
LPELGEPFSLLIDEMVPEEDGKEIEIACIGGLCQLLNICADVIYLRKDYDTFKIERYPNETGKPDLVILRKAAHFLSIIL
DSKKSIEERTNELGKDRISSPADVPPMTQSVTQESFSRKWLFALLALAILGALYYFFNKN

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF
VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

The proteins were purified in 20 mM TRIS pH 7.5, 150 mM NaCl, 2mM DTT and mixed in a 1:1.1 (Protease:ubiquitin) ratio. Reservoir: 0.2 M Magnesium format dihydrate, 20 % w/v PEG 3350, 0.02 M EDTA Protein and reservoir were mixed in a ratio of 1 ul : 2 ul.

AlphaFold2; custom version (https://github.com/muthoff/ComplexFold)

Deubiquitinase, papain-fold, OTU, HYDROLASE, swapped complex

(chain "B" and (resid 1 through 100 or resid 102 through 152))

(chain "D" and (resid 1 through 72 or resid 75 through 100 or resid 102 through 152))

MSLPVKERPDAIYTFEGKTYENTSFSKTGIPIVGQPLKMEAYVHKEYTHVTSLEGKRFKSQLEEAAKIYGEQLHEIQGDG
NCLTTAFATSFLYLLNGNATLIATFDNILIGLDAHKNIPPVRQTIEKLKVKNDLELKQILASNETMFAFSSVIRHLARQK
LPELGEPFSLLIDEMVPEEDGKEIEIACIGGLCQLLNICADVIYLRKDYDTFKIERYPNETGKPDLVILRKAAHFLSIIL
DSKKSIEERTNELGKDRISSPADVPPMTQSVTQESFSRKWLFALLALAILGALYYFFNKN