SASDC54: Envelope of Col H PKD-PKD-CBD complexed with mini-collagen

基本情報

• 登録情報: データベース: SASBDB / ID: SASDC54

試料

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

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

機能・相同性

分子機能:

tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / タンパク質分解 / zinc ion binding / extracellular region

ドメイン・相同性:

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

構成要素:

Collagenase ColH

• 生物種: Hathewaya histolytica (Clostridium histolyticum); synthetic construct (人工物)
• 引用: ジャーナル: FEBS J / 年: 2018; タイトル: Ca -induced orientation of tandem collagen binding domains from clostridial collagenase ColG permits two opposing functions of collagen fibril formation and retardation.; 著者: Perry Caviness / Ryan Bauer / Keisuke Tanaka / Katarzyna Janowska / Jeffrey Randall Roeser / Dawn Harter / Jes Sanders / Christopher Ruth / Osamu Matsushita / Joshua Sakon / ; 要旨: 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.

登録者

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

モデル

• モデル #1285: ; タイプ: dummy / ダミー原子の半径: 2.50 A / カイ2乗値: 3.217 / P-value: 0.000003; 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: Envelope of Col H PKD-PKD-CBD complexed with mini-collagen; 試料濃度: 1.00-5.00 / Entity id: 675 / 677
• バッファ: 名称: 50 mM Hepes 100 mM NaCl 5 mM CaCl2 / pH: 7.5

要素 #675

名称: ColH / タイプ: protein / 記述: ColH protein / 分子量: 33.727 / 分子数: 1 / 由来: Hathewaya histolytica (Clostridium histolyticum) / 参照: UniProt: Q46085
配列:

lpnegdskns lpygkingty kgtekekikf ssegsfdpdg kivsyewdfg dgnksneenp ehsydkvgty tvklkvtddk gessvsttta eikdlsenkl pviymhvpks galnqkvvfy gkgtydpdgs iagyqwdfgd gsdfsseqnp shvytkkgey tvtlrvmdss gqmsektmki kitdpvypig tekepnnske tasgpivpgi pvsgtients dqdyfyfdvi tpgevkidin klgyggatwv vydennnavs yatddgqnls gkfkadkpgr yyihlymfng sympyrinie gsvgr

要素 #677

タイプ: protein / 記述: Collagenous Peptide model [(PPG)10] / 分子量: 3.21 / 分子数: 3 / 由来: synthetic construct
配列:

PPGPPGPPGP PGPPGPPGPP GPPGPPGPPG

実験情報

• ビーム: 設備名称: Advanced Light Source (ALS) 12.3.1 (SIBYLS) / 地域: Berkeley, CA / 国: USA / 線源: X-ray synchrotronシンクロトロン / 波長: 0.113 Å
• 検出器: 名称: Pilatus3 X 2M / Pixsize x: 172 mm

スキャン

タイトル: Envelope of Col H PKD-PKD-CBD complexed with mini-collagen
測定日: 2016年10月12日 / 保管温度: 4 °C / セル温度: 10 °C / 照射時間: 0.3 sec. / フレーム数: 33 / 単位: 1/A /

	Min	Max
Q	0.0125	0.3575

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 407 /

	Min	Max
Q	0.014215	0.240521
P(R) point	1	407
R	0	141.6

結果

カーブのタイプ: extrapolated
コメント: Scattering for samples with concentrations of 4 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).

	実験値	Porod
分子量	46.613 kDa	-
体積	-	38 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	25.76	0.095	24.648	0.21
慣性半径, Rg	3.66 nm	0.02	3.321 nm	0.082

	Min	Max
D	-	14.16
Guinier point	4	48