Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni.
Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni.
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人alpha2,3-溶解酶的倍数识别和比较模型揭示了它们与弯曲杆菌的序列和结构相似性。
DOI：
10.1186/1472-6807-6-9
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发表时间：
2006-04-19
影响因子：
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通讯作者：
Balaji, Petety V
中科院分区：
文献类型：
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作者：
Sujatha, M S;Balaji, Petety V
迄今为止，尚未确定真核唾液酸转移酶 (SiaTs) 的 3-D 结构。 BLAST 和 PSI-BLAST 等序列比对算法无法从蛋白质数据库中检测到这些酶的同源物。因此，SiaT 属于 CASP 实验中的硬/中目标类别。当前工作的目标是使用折叠识别和比较建模方法对人类 SiaT 的 3-D 结构进行建模，这些 SiaT 以 α2,3-连接方式（即 ST3Gal I、II、III、IV、V 和 VI）转移唾液酸。这六种酶之间的成对序列相似性范围为 41% 至 63%。与序列相似性服务器不同，折叠识别服务器将 CstII（来自空肠弯曲杆菌的 α2,3/8 双活性 SiaT）识别为所有 6 个 ST3Gals 的同源物； CstII 和 ST3Gals 之间的序列相似性水平仅为 15-20%，并且相似性仅限于 ST3Gals 明确表征的基序区域。导出整个 ST3Gal 序列的模板-目标序列比对并不简单：折叠识别服务器无法找到 L 基序之前的区域以及 L 和 S 基序之间的区域的模板。确定了多个结构模板来对这些区域进行建模，并且必须迭代地执行模板识别-建模-评估以选择最合适的模板。建模的结构具有可接受的立体化学性质，并且还能够为文献中报道的一些定点诱变结果提供定性合理化。除了预测模型之外，本研究的一个意外但有价值的发现是家族 GT42 和家族 GT29 SiaT 的顺序和结构相关性。建模的 3-D 结构可用于对接和其他建模研究，以及合理识别要突变的残基，以赋予所需的特性，例如改变的稳定性、底物特异性等。文献中的一些研究集中在开发用于蛋白质 3-D 结构的大规模/自动建模的工具和/或服务器。相比之下，本研究侧重于对生物化学家感兴趣的特定蛋白质的 3-D 结构进行建模，并说明相关的困难。它还能够在两个不同家族的唾液酸转移酶之间建立序列/结构关系。
The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs) has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate specificity, etc. Several studies in literature have focused on the development of tools and/or servers for the large-scale/automated modeling of 3-D structures of proteins. In contrast, the present study focuses on modeling the 3-D structure of a specific protein of interest to a biochemist and illustrates the associated difficulties. It is also able to establish a sequence/structure relationship between sialyltransferases of two distinct families.