Elucidating Collagen Degradation Synergy between Col G and Col H from Hathewaya (Clostridium) histolytica and Identifying novel structural features in HPT and REC domains from VarS histidine kinase in V. alginolyticus

Perry Caviness, University of Arkansas PhD thesis 28030553 (2020) URL

SASDJV6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser bound to triple helical collagen like-peptide

Collagen like-peptide [GPRG(POG)13]
Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser)
MWexperimental 56 kDa
MWexpected 44 kDa
VPorod 79 nm3
log I(s) 3.57×101 3.57×100 3.57×10-1 3.57×10-2
Collagen like-peptide [GPRG(POG)13] Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) small angle scattering data  s, nm-1
ln I(s)
Collagen like-peptide [GPRG(POG)13] Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) Guinier plot ln 3.58×101 Rg: 4.4 nm 0 (4.4 nm)-2 s2
(sRg)2I(s)/I(0)
Collagen like-peptide [GPRG(POG)13] Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) Kratky plot 1.104 0 3 sRg
p(r)
Collagen like-peptide [GPRG(POG)13] Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) pair distance distribution function Rg: 5.0 nm 0 Dmax: 21 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Collagen like-peptide [GPRG(POG)13] Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) DAMFILT model
Collagen like-peptide [GPRG(POG)13] Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) DAMFILT model

Synchrotron SAXS data from solutions of Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser bound to triple helical collagen like-peptide in 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 2 mg/ml were measured at 10°C. 50 successive 0.300 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 low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

Storage temperature = UNKNOWN

Collagen like-peptide [GPRG(POG)13]
Mol. type   Protein
Olig. state   Trimer
Mon. MW   3.7 kDa
Sequence   FASTA
 
Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) (ColH)
Mol. type   Protein
Organism   Hathewaya histolytica
Olig. state   Monomer
Mon. MW   33.5 kDa
 
UniProt   Q46085 (718-1021)
Sequence   FASTA