SASDC44: Envelope of Col H PKD-CBD complexed with mini-collagen

Basic information

• Entry: Database: SASBDB / ID: SASDC44

Sample

Envelope of Col H PKD-CBD complexed with mini-collagen

• ColH protein (protein), ColH, Hathewaya histolytica (Clostridium histolyticum)
• Collagenous Peptide model [(PPG)10] (protein), synthetic construct

Function / homology

Function:

tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region

Domain/homology:

Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold

Component:

Collagenase ColH

• Biological species: Hathewaya histolytica (Clostridium histolyticum); synthetic construct (others)
• Citation: Journal: FEBS J / Year: 2018; Title: Ca -induced orientation of tandem collagen binding domains from clostridial collagenase ColG permits two opposing functions of collagen fibril formation and retardation.; Authors: Perry Caviness / Ryan Bauer / Keisuke Tanaka / Katarzyna Janowska / Jeffrey Randall Roeser / Dawn Harter / Jes Sanders / Christopher Ruth / Osamu Matsushita / Joshua Sakon / ; Abstract: To penetrate host tissues, histotoxic clostridia secrete virulence factors including enzymes to hydrolyze extracellular matrix. Clostridium histolyticum, recently renamed as Hathewaya histolytica, produces two classes of collagenase (ColG and ColH). The high-speed AFM study showed that ColG collagenase moves unidirectionally to plane collagen fibril and rebundles fibril when stalled . The structural explanation of the roles for the tandem collagen-binding segment (CBDs) is illuminated by its calcium-bound crystal structure at 1.9 Å resolution (R = 15.0%; R = 19.6%). Activation may involve calcium-dependent domain rearrangement supported by both small-angle X-ray scattering and size exclusion chromatography. At pCa ≥ 5 (pCa = -log[Ca ]), the tandem CBD adopts an extended conformation that may facilitate secretion from the bacterium. At pCa ≤ 4, the compact structure seen in the crystal structure is adopted. This arrangement positions the two binding surfaces ~ 55 Å apart, and possibly ushers ColG along tropocollagen molecules that allow for unidirectional movement. A sequential binding mode where tighter binding CBD2 binds first could aid in processivity as well. Switch from processive collagenolysis to fibril rearrangement could be concentration dependent. Collagen fibril formation is retarded at 1 : 1 molar ratio of tandem CBD to collagen. Tandem CBD may help isolate a tropocollagen molecule from a fibril at this ratio. At 0.1 : 1 to 0.5 : 1 molar ratios fibril self-assembly was accelerated. Gain of function as a result of gene duplication of CBD for the M9B enzymes is speculated. The binding and activation modes described here will aid in drug delivery design.; ACCESSION CODES: The full atomic coordinates of the tandem CBD and its corresponding structure factor amplitudes have been deposited in the Protein Data Bank (PDB accession code 5IKU). Small-angle X-ray scattering data and corresponding ab initio models have been submitted to the Small Angle Scattering Biological Data Bank (SASBDB). Accession codes CL2, collagenase module 2, CN2, CP2 are assigned to envelopes for tandem CBD at -log[Ca ] (pCa) 3, 4, 5, and 6, respectively. Accession code DC64 was assigned to the complex of polycystic kidney disease-CBD1-CBD2 with mini-collagen.

Contact author

• Perry Caviness (University of Arkansas, Fayetteville, AR, USA)

Models

• Model #1284: ; Type: dummy / Radius of dummy atoms: 2.50 A / Chi-square value: 5.283 / P-value: 0.212205; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Envelope of Col H PKD-CBD complexed with mini-collagen; Specimen concentration: 1.00-5.00 / Entity id: 673 / 674
• Buffer: Name: 50 mM Hepes 100 mM NaCl 5 mM CaCl2 / pH: 7.5

Entity #673

Name: ColH / Type: protein / Description: ColH protein / Formula weight: 23.94 / Num. of mol.: 1 / Source: Hathewaya histolytica (Clostridium histolyticum) / References: UniProt: Q46085
Sequence:

aeikdlsenk lpviymhvpk sgalnqkvvf ygkgtydpdg siagyqwdfg dgsdfsseqn pshvytkkge ytvtlrvmds sgqmsektmk ikitdpvypi gtekepnnsk etasgpivpg ipvsgtient sdqdyfyfdv itpgevkidi nklgyggatw vvydennnav syatddgqnl sgkfkadkpg ryyihlymfn gsympyrini egsvgr

Entity #674

Type: protein / Description: Collagenous Peptide model [(PPG)10] / Formula weight: 3.05 / Num. of mol.: 3 / Source: synthetic construct
Sequence:

PPGPPGPPGP PGPPGPPGPP GPPGPPGPPG

Experimental information

• Beam: Instrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS); City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.113 Å
• Detector: Name: Pilatus3 X 2M / Pixsize x: 172 mm

Scan

Title: Envelope of Col H PKD-CBD complexed with mini-collagen
Measurement date: Oct 12, 2016 / Storage temperature: 4 °C / Cell temperature: 10 °C / Exposure time: 0.3 sec. / Number of frames: 33 / Unit: 1/A /

	Min	Max
Q	0.0125	0.3575

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 495 /

	Min	Max
Q	0.021462	0.296807
P(R) point	1	495
R	0	121.5

Result

Type of curve: extrapolated
Comments: Scattering for samples with concentrations of 5 mg/ml, 3 mg/ml and 1 mg/ml were averaged. Each of the average scattering curves are used to extrapolate towards infinite dilution. The scattering curve at infinite dilution was used to generate the SAXS model that represents the averaged spatial disposition of the complex in solution (DAMFILT).

	Experimental	Porod
MW	36.8 kDa	-
Volume	-	28 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	12.83	0.05	12.3491	0.0624529
Radius of gyration, Rg	2.985 nm	0.02	2.693 nm	0.078

	Min	Max
D	-	12
Guinier point	17	65