In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations.

Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.

荧光素酶、芳基 - 和脂肪酰基辅酶A合成酶以及非核糖体肽合成酶蛋白属于I类腺苷酸形成酶超家族。腺苷酸形成酶催化的反应通过腺苷酸化和硫酯化两步过程进行分类。尽管所有这些蛋白都执行类似的两步过程，但每个家族可能执行该过程以产生完全不同的结果。例如，荧光素酶蛋白进行腺苷酸化和氧化以产生萤火虫中发现的绿色荧光，而脂肪酰基辅酶A合成酶与辅酶A进行腺苷酸化和硫酯化，以协助涉及脂肪酸的代谢过程。本研究比对了总共374个属于腺苷酸形成超家族的序列。对这些序列的分析揭示了在所有序列中完全保守的5个残基，以及在至少60%的比对序列中保守的另外78个残基。保守位置参与镁离子和AMP结合以及维持酶结构。此外，还鉴定出了10个包含大多数保守残基的保守序列基序。使用系统发育树将序列划分为9个不同的组。最后，组熵分析确定了每个酶组特有的新的保守特征。在多个组中确定的常见的组特异性位置包括对协调AMP和与辅酶A结合的产物至关重要的位置、一个控制活性位点形状的位置以及通过氢键和疏水相互作用帮助维持酶结构的位置。这些位置可作为未来研究的极佳靶点。