Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece.
Department of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece.
Biomolecules. 2024 Mar 8;14(3):325. doi: 10.3390/biom14030325.
Enzymes of the carbohydrate esterase family 4 (CE4) deacetylate a broad range of substrates, including linear, branched and mesh-like polysaccharides. Although they are enzymes of variable amino acid sequence length, they all comprise the conserved catalytic domain NodB. NodB carries the metal binding and active site residues and is characterized by a set of conserved sequence motifs, which are linked to the deacetylation activity. Besides a non-structured, flexible peptide of variable length that precedes NodB, several members of the CE4 family contain additional domains whose function or contribution to substrate specificity are not efficiently characterized. Evidence suggests that CE4 family members comprising solely the NodB domain have developed features linked to a variety of substrate specificities. To understand the NodB-based substrate diversity within the CE4 family, we perform a comparative analysis of all NodB domains structurally characterized so far. We show that amino acid sequence variations, topology diversities and excursions away from the framework structure give rise to different NodB domain classes associated with different substrate specificities and particular functions within and beyond the CE4 family. Our work reveals a link between specific NodB domain characteristics and substrate recognition. Thus, the details of the fold are clarified, and the structural basis of its variations is deciphered and associated with function. The conclusions of this work are also used to make predictions and propose specific functions for biochemically/enzymatically uncharacterized NodB-containing proteins, which have generally been considered as putative CE4 deacetylases. We show that some of them probably belong to different enzymatic families.
碳水化合物酯酶家族 4（CE4）的酶可以去乙酰化广泛的底物，包括线性、支链和网状多糖。尽管它们的氨基酸序列长度不同，但都包含保守的催化结构域 NodB。NodB 携带金属结合和活性位点残基，并具有一组保守的序列基序，这些基序与去乙酰化活性相关。除了 NodB 之前的可变长度非结构、柔性肽外，CE4 家族的几个成员还包含其他结构域，其功能或对底物特异性的贡献尚未得到有效表征。有证据表明，仅包含 NodB 结构域的 CE4 家族成员具有与各种底物特异性相关的特征。为了了解 CE4 家族中基于 NodB 的底物多样性，我们对迄今为止所有结构上已确定的 NodB 结构域进行了比较分析。我们表明，氨基酸序列变化、拓扑多样性和远离框架结构的偏移导致不同的 NodB 结构域类别，这些类别与不同的底物特异性以及 CE4 家族内外的特定功能相关。我们的工作揭示了特定 NodB 结构域特征与底物识别之间的联系。因此，阐明了折叠的细节，并解释了其变化的结构基础，并与功能相关联。这项工作的结论还用于对生物化学/酶学上未表征的含 NodB 蛋白进行预测，并提出特定的功能，这些蛋白通常被认为是假定的 CE4 去乙酰酶。我们表明，其中一些可能属于不同的酶家族。
