Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden.
BMC Genomics. 2009 Dec 8;10:589. doi: 10.1186/1471-2164-10-589.
Ribonucleotide reductases (RNRs) catalyse the only known de novo pathway for deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. While ribonucleotide reduction has a single evolutionary origin, significant differences between RNRs nevertheless exist, notably in cofactor requirements, subunit composition and allosteric regulation. These differences result in distinct operational constraints (anaerobicity, iron/oxygen dependence and cobalamin dependence), and form the basis for the classification of RNRs into three classes.
In RNRdb (Ribonucleotide Reductase database), we have collated and curated all known RNR protein sequences with the aim of providing a resource for exploration of RNR diversity and distribution. By comparing expert manual annotations with annotations stored in Genbank, we find that significant inaccuracies exist in larger databases. To our surprise, only 23% of protein sequences included in RNRdb are correctly annotated across the key attributes of class, role and function, with 17% being incorrectly annotated across all three categories. This illustrates the utility of specialist databases for applications where a high degree of annotation accuracy may be important. The database houses information on annotation, distribution and diversity of RNRs, and links to solved RNR structures, and can be searched through a BLAST interface. RNRdb is accessible through a public web interface at http://rnrdb.molbio.su.se.
RNRdb is a specialist database that provides a reliable annotation and classification resource for RNR proteins, as well as a tool to explore distribution patterns of RNR classes. The recent expansion in available genome sequence data have provided us with a picture of RNR distribution that is more complex than believed only a few years ago; our database indicates that RNRs of all three classes are found across all three cellular domains. Moreover, we find a number of organisms that encode all three classes.
核苷酸还原酶（RNRs）催化脱氧核苷酸合成的唯一已知从头途径，因此对基于 DNA 的生命至关重要。虽然核苷酸还原具有单一的进化起源，但 RNRs 之间仍然存在显著差异，特别是在辅助因子要求、亚基组成和变构调节方面。这些差异导致了不同的操作限制（厌氧性、铁/氧依赖性和钴胺素依赖性），并为 RNR 分为三类奠定了基础。
在 RNRdb（核苷酸还原酶数据库）中，我们收集和整理了所有已知的 RNR 蛋白质序列，旨在为探索 RNR 多样性和分布提供资源。通过比较专家手动注释和存储在 Genbank 中的注释，我们发现较大的数据库中存在显著的不准确之处。令我们惊讶的是，RNRdb 中包含的蛋白质序列只有 23%在类、角色和功能的关键属性上得到正确注释，17%在所有三个类别上都被错误注释。这说明了专门数据库在可能需要高度注释准确性的应用中的实用性。该数据库存储有关 RNR 的注释、分布和多样性的信息，并链接到已解决的 RNR 结构，并且可以通过 BLAST 接口进行搜索。RNRdb 可通过公共网络界面访问，网址为 http://rnrdb.molbio.su.se。
RNRdb 是一个专门的数据库，为 RNR 蛋白质提供了可靠的注释和分类资源，也是探索 RNR 类分布模式的工具。近年来可用基因组序列数据的扩展使我们对 RNR 分布的了解比几年前更为复杂；我们的数据库表明，所有三个类别的 RNR 都存在于所有三个细胞域中。此外，我们发现许多生物体编码了所有三个类别。
