The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP in Mycobacterium smegmatis

Chen H, Li N, Luo Y, Jiang Y, Zhou C, Chen Y, Li Q, Biochemical Journal 475(7):1295-1308 (2018) DOI

SASDCH9 – Bifunctional enzyme responsible for the synthesis and hydrolysis of c-di-GMP (DcpA) with GDP

Sensory box/response regulator
MWexperimental 156 kDa
MWexpected 136 kDa
VPorod 299 nm3
log I(s) 3.37×102 3.37×101 3.37×100 3.37×10-1
Sensory box/response regulator small angle scattering data  s, nm-1
ln I(s)
Sensory box/response regulator Guinier plot ln 3.37×102 Rg: 5.0 nm 0 (5.0 nm)-2 s2
Sensory box/response regulator Kratky plot 1.104 0 3 sRg
Sensory box/response regulator pair distance distribution function Rg: 5.2 nm 0 Dmax: 20 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Sensory box/response regulator CORAL model

log I(s)
 s, nm-1
Sensory box/response regulator DAMMIF model

Synchrotron SAXS data from solutions of bifunctional enzyme responsible for the synthesis and hydrolysis of c-di-GMP (DcpA) with GDP in 20 mM HEPES, 100 mM NaCl, 5% glycerol, 2 mM MgCl2, pH 7.5, were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Pilatus 1M detector at a sample-detector distance of 2.3 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 20°C. 20 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 and the different curves were scaled for protein concentration.

Sensory box/response regulator
Mol. type   Protein
Organism   Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Olig. state   Dimer
Mon. MW   67.8 kDa
UniProt   A0QUG3
Sequence   FASTA
PDB code   4RNH