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

基本情報

• 登録情報: データベース: SASBDB / ID: SASDAG6

試料

K1K2 domains of Kgp gingipain

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

機能・相同性

分子機能:

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

ドメイン・相同性:

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

構成要素:

Lys-gingipain W83

• 生物種: Porphyromonas gingivalis W83 (バクテリア)
• 引用: ジャーナル: Mol Microbiol / 年: 2011; タイトル: The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis.; 著者: Nan Li / Peter Yun / Cy M Jeffries / David Langley / Roland Gamsjaeger / W Bret Church / Neil Hunter / Charles A Collyer / ; 要旨: 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.

登録者

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

モデル

• モデル #187: ; タイプ: mix / ダミー原子の半径: 1.90 A / カイ2乗値: 0.509796; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: K1K2 domains of Kgp gingipain / Contrast: 2.975 / Specific vol: 0.7371 / 試料濃度: 2.89 mg/ml / 濃度測定法: A280 nm
• バッファ: 名称: 10 mM TRIS 150 mM NaCl / 濃度: 10.00 mM / pH: 7.6 / 組成: NaCl 150.000 mM

要素 #125

名称: K1K2 / タイプ: protein
記述: K1K2 adhesin modules of lysine-specific (Kgp) gingipain
分子量: 38.4 / 分子数: 1 / 由来: Porphyromonas gingivalis W83 / 参照: UniProt: Q51817
配列:

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

実験情報

• ビーム: 設備名称: University of Sydney Anton Paar SAXSess / 地域: Sydney / 国: Australia / 形状: Line collimation / 線源: X-ray in house / 波長: 0.1542 Å / スペクトロメータ・検出器間距離: 0.309 mm
• 検出器: 名称: Roper Scientific PI-SCX:4300 / タイプ: KAF 2084 x 2084 SCX CCD / Pixsize x: 24 mm

スキャン

タイトル: K1K2 domains of Kgp gingipain / 測定日: 2010年8月15日 / 保管温度: 15 °C / セル温度: 15 °C / 照射時間: 10 sec. / フレーム数: 1080 / 単位: 1/nm /

	Min	Max
Q	0.0977	3.712

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.5a / ポイント数: 368 /

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

結果

カーブのタイプ: single_conc / Standard: water
コメント: 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).

	実験値	Standard
分子量	40.6 kDa	40.6 kDa

	P(R)	Guinier
前方散乱 I0	0.094	0.093
慣性半径, Rg	3.02 nm	2.92 nm

	Min	Max
D	-	9.5
Guinier point	1	35