RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to GenBank

Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden.
BMC Genomics (Impact Factor: 3.99). 12/2009; 10(1):589. DOI: 10.1186/1471-2164-10-589
Source: PubMed


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
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.

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    • "during adaptation to an obligate intracellular lifestyle and now derive deoxyribonucleotides from their host) (Lundin et al. 2010, 2009). Thus, if the reverse DERA reaction ever was used for deoxyribonucleotide synthesis, it has long ceased to perform this function. "
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    ABSTRACT: All life generates deoxyribonucleotides, the building blocks of DNA, via ribonucleotide reductases (RNRs). The complexity of this reaction suggests it did not evolve until well after the advent of templated protein synthesis, which in turn suggests DNA evolved later than both RNA and templated protein synthesis. However, deoxyribonucleotides may have first been synthesised via an alternative, chemically simpler route—the reversal of the deoxyriboaldolase (DERA) step in deoxyribonucleotide salvage. In light of recent work demonstrating that this reaction can drive synthesis of deoxyribonucleosides, we consider what pressures early adoption of this pathway would have placed on cell metabolism. This in turn provides a rationale for the replacement of DERA-dependent DNA production by RNR-dependent production. Electronic supplementary material The online version of this article (doi:10.1007/s00239-014-9656-6) contains supplementary material, which is available to authorized users.
    Full-text · Article · Nov 2014 · Journal of Molecular Evolution
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    • "Typically two copies of the NrdR-box are consistently detected in the promoter region of different nrd genes, with specific spacing corresponding to an integral number of turns in the double DNA helix. Currently, NrdR has been classified as a member of a highly conserved family of proteins confined exclusively to prokaryotes, eubacteria, and some archaea (Lundin et al., 2009). NrdR is a 150– 200-amino acid protein harboring two protein domains: an Nterminal zinc finger like DNA-binding domain and a C-terminal ATP-cone domain that binds nucleotides (Figure 4A). "
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    ABSTRACT: Ribonucleotide reductase (RNR) is a key enzyme that mediates the synthesis of deoxyribonucleotides, the DNA precursors, for DNA synthesis in every living cell. This enzyme converts ribonucleotides to deoxyribonucleotides, the building blocks for DNA replication, and repair. Clearly, RNR enzymes have contributed to the appearance of genetic material that exists today, being essential for the evolution of all organisms on Earth. The strict control of RNR activity and dNTP pool sizes is important, as pool imbalances increase mutation rates, replication anomalies, and genome instability. Thus, RNR activity should be finely regulated allosterically and at the transcriptional level. In this review we examine the distribution, the evolution, and the genetic regulation of bacterial RNRs. Moreover, this enzyme can be considered an ideal target for anti-proliferative compounds designed to inhibit cell replication in eukaryotic cells (cancer cells), parasites, viruses, and bacteria.
    Full-text · Article · Apr 2014 · Frontiers in Cellular and Infection Microbiology
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    • "A second copy of the small subunit gene (PfR4) was later documented in P. falciparum and found to be highly divergent from the standard PfR2 (a typical NrdB protein) (Bracchi- Ricard et al. 2005). The recent completion of several Apicomplexa genome projects has revealed the presence of two NrdB homologous proteins in several of these organisms , a subset of which are represented in the Ribonucleotide Reductase database (RNRdb) (Lundin et al. 2009). "
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    ABSTRACT: Apicomplexa are protist parasites of tremendous medical and economic importance, causing millions of deaths and billions of dollars in losses each year. Apicomplexan-related diseases may be controlled via inhibition of essential enzymes. Ribonucleotide reductase (RNR) provides the only de novo means of synthesizing deoxyribonucleotides, essential precursors for DNA replication and repair. RNR has long been the target of antibacterial and antiviral therapeutics. However, targeting this ubiquitous protein in eukaryotic pathogens may be problematic unless these proteins differ significantly from that of their respective host. The typical eukaryotic RNR enzymes belong to class Ia, and the holoenzyme consists minimally of two R1 and two R2 subunits (α2β2). We generated a comparative, annotated, structure-based, multiple-sequence alignment of R2 subunits, identified a clade of R2 subunits unique to Apicomplexa, and determined its phylogenetic position. Our analyses revealed that the apicomplexan-specific sequences share characteristics with both class I R2 and R2lox proteins. The putative radical-harboring residue, essential for the reduction reaction by class Ia R2-containing holoenzymes, was not conserved within this group. Phylogenetic analyses suggest that class Ia subunits are not monophyletic and consistently placed the apicomplexan-specific clade sister to the remaining class Ia eukaryote R2 subunits. Our research suggests that the novel apicomplexan R2 subunit may be a promising candidate for chemotherapeutic-induced inhibition as it differs greatly from known eukaryotic host RNRs and may be specifically targeted. Electronic supplementary material The online version of this article (doi:10.1007/s00239-013-9583-y) contains supplementary material, which is available to authorized users.
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