Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.

Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Gräwert TW, Knebel A, Svergun DI, Kulathu Y, Mol Cell (2021) Europe PMC

SASDJ93 – Ubiquitin carboxyl-terminal hydrolase, MINDY2, wild-type apo-form

Ubiquitin carboxyl-terminal hydrolase MINDY-2
MWexperimental 28 kDa
MWexpected 31 kDa
VPorod 45 nm3
log I(s) 1.22×103 1.22×102 1.22×101 1.22×100
Ubiquitin carboxyl-terminal hydrolase MINDY-2 small angle scattering data  s, nm-1
ln I(s)
Ubiquitin carboxyl-terminal hydrolase MINDY-2 Guinier plot ln 1.23×103 Rg: 2.1 nm 0 (2.1 nm)-2 s2
(sRg)2I(s)/I(0)
Ubiquitin carboxyl-terminal hydrolase MINDY-2 Kratky plot 1.104 0 √3 sRg
p(r)
Ubiquitin carboxyl-terminal hydrolase MINDY-2 pair distance distribution function Rg: 2.2 nm 0 Dmax: 6.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Ubiquitin carboxyl-terminal hydrolase MINDY-2 CUSTOM IN-HOUSE model
Synchrotron SAXS data from solutions of MINDY2 in 20 mM HEPES, 100 mM NaCl, 5 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.12 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 75.00 μl sample at 8.8 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 3000 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The experimental MW is based on Porod volume.

Ubiquitin carboxyl-terminal hydrolase MINDY-2 (MINDY2 apo)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   31.0 kDa
 
UniProt   Q8NBR6 (241-504)
Sequence   FASTA