Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Science, Rutgers the State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, USA.
Integr Biol (Camb). 2012 Jul;4(7):765-77. doi: 10.1039/c2ib00131d. Epub 2012 Apr 5.
Non-equilibrium catalysis of electron transfer reactions (i.e. redox) regulates the flux of key elements found in biological macromolecules. The enzymes responsible, oxidoreductases, contain specific transition metals in poorly sequence-conserved domains. These domains evolved ∼2.4 billion years ago in microbes and spread across the tree of life. We lack understanding of how oxidoreductases evolved; divergence of sequences makes identification difficult. We developed a method to recognise the various versions of these enzyme-domains in unannotated sequence-space. Often, homology is used to transfer function annotations from experimentally resolved domains to unannotated sequences. Unreliability of inferring homology below 30% sequence identity limits single-sequence based searches. Misaligned functional sites may compromise annotation transfer from even very similar sequences. Combining profile-based searches with knowledge of functional sites could improve domain detection accuracy. Here we present an approach that enhances the search for redox domains using catalytic site annotations. From the scientific literature, we validated annotations of 104 InterPro domains indicated as using "transition metals in redox reactions." These domains mediate electron transfer in 20% of oxidoreductases, primarily employing iron, copper and molybdenum. We used the experimentally identified catalytic residues in these domains to validate sequence alignment-based protein function annotations. Our method, TrAnsFuSE, is 11% and 14% more accurate than PSI-BLAST and InterPro, respectively. Moreover, it is robust for use with other functional residues-we attain higher accuracy at comparable coverage using metal binding, in addition to catalytic, sites. TrAnsFuSE can be used to focus the study of the vast amounts of unannotated sequencing data from meta-/genome projects.
非平衡态电子转移反应（即氧化还原）催化调节生物大分子中关键元素的流动。负责的氧化还原酶在序列保守性差的特定区域含有特定的过渡金属。这些区域大约在 24 亿年前在微生物中进化，并在生命之树上传播。我们缺乏对氧化还原酶进化的理解；序列的分歧使得鉴定变得困难。我们开发了一种在未注释的序列空间中识别各种酶域版本的方法。通常，同源性用于将功能注释从实验解析的域转移到未注释的序列。低于 30%序列同一性的同源性推断的可靠性限制了基于单一序列的搜索。即使非常相似的序列，功能位点的未对齐也可能破坏注释的转移。将基于轮廓的搜索与功能位点的知识相结合可以提高域检测的准确性。在这里，我们提出了一种使用催化位点注释来增强氧化还原域搜索的方法。从科学文献中，我们验证了 104 个 InterPro 域的注释，这些域被指示为在“氧化还原反应中使用过渡金属”。这些域在 20%的氧化还原酶中介导电子转移，主要使用铁、铜和钼。我们使用这些域中实验鉴定的催化残基来验证基于序列比对的蛋白质功能注释。我们的方法 TrAnsFuSE 比 PSI-BLAST 和 InterPro 分别准确 11%和 14%。此外，它对于使用其他功能残基也很稳健-我们在使用金属结合的同时，在可比的覆盖率下实现了更高的准确性，除了催化位点。TrAnsFuSE 可用于集中研究来自元/基因组项目的大量未注释的测序数据。
