SASDAG6: K1K2 domains of Kgp gingipain (K1K2 adhesin modules of lysine-spe...

Basic information

• Entry: Database: SASBDB / ID: SASDAG6

Sample

K1K2 domains of Kgp gingipain

• K1K2 adhesin modules of lysine-specific (Kgp) gingipain (protein), K1K2, Porphyromonas gingivalis W83

Function / homology

Function:

gingipain K / hemolysis in another organism / cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region

Domain/homology:

Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain / Peptidase family C25 / Caspase-like domain superfamily / Immunoglobulin-like fold

Component:

Lys-gingipain W83

• Biological species: Porphyromonas gingivalis W83 (bacteria)
• Citation: Journal: Mol Microbiol / Year: 2011; Title: The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis.; Authors: Nan Li / Peter Yun / Cy M Jeffries / David Langley / Roland Gamsjaeger / W Bret Church / Neil Hunter / Charles A Collyer / ; Abstract: High-molecular-weight arginine- and lysine-specific (Kgp) gingipains are essential virulence factors expressed by the oral pathogen Porphyromonas gingivalis. Haemagglutinin/adhesin (HA) regions of these proteases have been implicated in targeting catalytic domains to biological substrates and in other adhesive functions. We now report the crystal structure of the K3 adhesin domain/module of Kgp, which folds into the distinct β-jelly roll sandwich topology previously observed for K2. A conserved structural feature of K3, previously observed in the Kgp K2 module, is the half-way point anchoring of the surface exposed loops via an arginine residue found in otherwise highly variable sequences. Small-angle X-ray scattering data for the recombinant construct K1K2K3 confirmed a structure comprising a tandem repeat of three homologous modules, K1, K2 and K3 while also indicating an unusual 'y'-shape arrangement of the modules connected by variable linker sequences. Only the K2 and K3 modules and a K1K2 construct were observed to be potently haemolytic. K2, K3 and the K1K2 construct showed preferential recognition of haem-albumin over albumin whereas only low affinity binding was detected for K1 and the K1K2K3 construct. The data indicate replication of some biological functions over the three adhesin domains of Kgp while other functions are restricted.

Contact author

• Cy M Jeffries (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #187: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.509796; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: K1K2 domains of Kgp gingipain / Contrast: 2.975 / Specific vol: 0.7371 / Specimen concentration: 2.89 mg/ml / Concentration method: A280 nm
• Buffer: Name: 10 mM TRIS 150 mM NaCl / Concentration: 10.00 mM / pH: 7.6 / Composition: NaCl 150.000 mM

Entity #125

Name: K1K2 / Type: protein
Description: K1K2 adhesin modules of lysine-specific (Kgp) gingipain
Formula weight: 38.4 / Num. of mol.: 1 / Source: Porphyromonas gingivalis W83 / References: UniProt: Q51817
Sequence:

GPLGSGTTLS ESFENGIPAS WKTIDADGDG HGWKPGNAPG IAGYNSNGCV YSESFLGGIG VLTPDNYLIT PALDLPNGGK LTFWVCAQDA NYASEHYAVY ASSTGNDASN FTNALLEETI TAKGVRSPKA IRGRIQGTWR QKTVDLPAGT KYVAFRHFQS TDMFYIDLDE VEIKANGKRA DFTETFESST HGEAPAEWTT IDADGDGQGW LCLSSGQLDW LTAHGGSNVV SSFSWNGMAL NPDNYLISKD VTGATKVKYY YAVNDGFPGD HYAVMISKTG TNAGDFTVVF EETPNGINKG GARFGLSTEA NGAKPQSVWI ERTVDLPAGT KYVAFRHYNC SDLNYILLDD IQFTMGG

Experimental information

• Beam: Instrument name: University of Sydney Anton Paar SAXSess / City: Sydney / 国: Australia / Shape: Line collimation / Type of source: X-ray in house / Wavelength: 0.1542 Å / Dist. spec. to detc.: 0.309 mm
• Detector: Name: Roper Scientific PI-SCX:4300 / Type: KAF 2084 x 2084 SCX CCD / Pixsize x: 24 mm

Scan

Title: K1K2 domains of Kgp gingipain / Measurement date: Aug 15, 2010 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 10 sec. / Number of frames: 1080 / Unit: 1/nm /

	Min	Max
Q	0.0977	3.712

Distance distribution function P(R)

Sofotware P(R): GNOM 4.5a / Number of points: 368 /

	Min	Max
Q	0.0977	3.712
P(R) point	1	368
R	0	9.5

Result

Type of curve: single_conc / Standard: water
Comments: The primary SAXS data displayed in this entry, and subsequent I(0), Rg and p(r) profile, take into account the beam-profile geometry correction (10 mm horizontal slit).

	Experimental	Standard
MW	40.6 kDa	40.6 kDa

	P(R)	Guinier
Forward scattering, I0	0.094	0.093
Radius of gyration, Rg	3.02 nm	2.92 nm

	Min	Max
D	-	9.5
Guinier point	1	35