Crystal Structure of a Bacterial Unsaturated Glucuronyl Hydrolase with Specificity for Heparin*
Crystal Structure of a Bacterial Unsaturated Glucuronyl Hydrolase with Specificity for Heparin*
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具有肝素特异性的细菌不饱和葡萄糖醛酸水解酶的晶体结构*
DOI：
10.1074/jbc.m113.522573
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
W. Hashimoto
中科院分区：
文献类型：
--
作者：
Y. Nakamichi;B. Mikami;K. Murata;W. Hashimoto
背景：细菌不饱和葡萄糖醛酸基水解酶（UGL）是完全降解宿主糖胺聚糖所必需的。结果：确定了肝素足杆菌UGL（Phep_2830）的晶体结构。结论：Phep_2830的口袋状结构和盖环参与了肝素二糖的识别。意义：这项工作有助于了解宿主细胞外基质成分的细菌降解。细胞外基质分子如糖胺聚糖（GAG）是一些致病细菌的典型靶标，其允许粘附于宿主细胞。细菌多糖裂解酶在β-消除反应中降解GAG，并且所得的不饱和二糖随后被不饱和葡糖醛酸基水解酶（UGL）降解为组成单糖。UGL底物根据糖苷键分为1，3-型和1，4-型。不饱和软骨素和肝素二糖分别是1，3-和1，4-型的典型成员。在这里，我们展示了细菌UGL与不饱和肝素二糖的反应模式，通过X射线晶体学，对接模拟和定点诱变。虽然链球菌和芽孢杆菌UGL对不饱和肝素二糖有活性，但它们更喜欢1，3-而不是1，4-型底物。降解GAG的肝素足杆菌的基因组编码13个UGL。其中，已知Phep_2830对不饱和肝素二糖具有特异性。Phep_2830的晶体结构在1.35-nm分辨率下测定。与链球菌和芽孢杆菌UGL的结构相比，在亚位点+1处的袋状结构和盖环是Phep_2830的特征。Phep_2830与不饱和肝素二糖的对接模拟表明，底物吡喃糖环的方向不同于不饱和软骨素二糖。不饱和肝素二糖的乙酰基很好地容纳在子位点+1的口袋中，并且盖环的芳香族残基是与底物堆叠相互作用所需的。因此，口袋和盖环的定点突变导致酶活性显著降低，表明口袋样结构和盖环参与UGL对1，4-型底物的识别。
Background: Bacterial unsaturated glucuronyl hydrolase (UGL) is essential for complete degradation of host glycosaminoglycans. Results: Crystal structure of Pedobacter heparinus UGL, Phep_2830 specific for heparin degradation, was determined. Conclusion: The pocket-like structure and lid loop of Phep_2830 are involved in heparin disaccharide recognition. Significance: This work contributes to understanding the bacterial degradation of host extracellular matrix components. Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in β-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by x-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and Bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35-Å resolution. In comparison with structures of streptococcal and Bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.
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影响因子：
2.9
作者：
James R. Myette;Z. Shriver;T. Kiziltepe;M. W. McLean;G. Venkataraman;R. Sasisekharan
通讯作者：
James R. Myette;Z. Shriver;T. Kiziltepe;M. W. McLean;G. Venkataraman;R. Sasisekharan
影响因子：
15.9
作者：
Esko, JD;Lindahl, U
通讯作者：
Lindahl, U
DOI：
10.1073/pnas.90.8.3660
发表时间：
1993-04-15
影响因子：
11.1
作者：
SASISEKHARAN, R;BULMER, M;LANGER, R
通讯作者：
LANGER, R
DOI：
10.1016/s1054-3589(05)53009-6
发表时间：
2006-01-01
期刊：
CHONDROITIN SULFATE: STRUCTURE, ROLE AND PHARMACOLOGICAL ACTIVITY
影响因子：
--
作者：
Linhardt, Robert J.;Avci, Fikri Y.;Cygler, Miroslaw
通讯作者：
Cygler, Miroslaw
影响因子：
3.9
作者：
Luo, Yongde;Huang, Xinqiang;McKeehan, Wallace L.
通讯作者：
McKeehan, Wallace L.