CAZyme3D:碳水化合物活性酶的3D结构数据库
N R Siva Shanmugam1, Yanbin Yin1
1Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
Journal of molecular biology
|February 17, 2025
概括
CAZyme3D是一个新的碳水化合物活性酶 (CAZymes) 3D蛋白质结构数据库. 它使用结构相似性来帮助发现新的CAZymes,改善健康,营养和生物能源方面的研究.
科学领域:
- 生物化学和结构生物学
- 生物信息学和计算生物学
- 酶学 是一种酶学.
背景情况:
- 碳水化合物活性酶 (CAZymes) 对于理解复杂的碳水化合物在人类健康,营养,肠道微生物群,生物能源,植物疾病和碳循环中的作用至关重要.
- 目前的CAZyme鉴定依赖于序列相似性,限制了远距离相关酶的发现.
- 在CAZymes的专用3D结构数据库中存在一个缺口,这阻碍了基于结构同质性的分析.
研究的目的:
- 开发CAZyme3D,为CAZymes提供一个全面的3D结构数据库,使其能够进行结构相似性搜索.
- 建立基于结构相似性的CAZymes的层次分类系统.
- 通过结构性比较,为发现新型CAZymes提供一个工具.
主要方法:
- 使用AlphaFold.生成了870,740个预测的3DCAZyme结构的大数据集.
- 对188,574个非冗余的CAZyme结构进行了基于结构相似性的聚类.
- 开发了一个等级分类,包括现有的CAZy级别和新的子类,结构集群 (SC) 组和SC级别.
- 实现了一个基于Web的工具,用于使用查询蛋白序列或PDB结构进行结构相似性搜索.
主要成果:
- CAZyme3D提供了预测CAZyme 3D结构的全面存储库.
- 结构聚类成功地将CAZymes组织成基于共享结构折叠的子类.
- 定义了新的分类 (SCs和SC组),与基于序列的子家族区分开来.
- 该平台允许用户对CAZyme3D数据库进行结构相似性搜索.
结论:
- CAZyme3D解决了对CAZymes.的专用3D结构数据库的需求.
- 结构分类为理解CAZyme关系提供了一个新的框架.
- CAZyme3D是通过结构分析发现新型CAZymes和功能注释的宝贵工具.
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