| Accession | GenProp0287 |
| Name | ribonucleotide reduction |
| Type | METAPATH |
| Description | The reduction of the ribose sugar of ribonucleotide triphosphates to deoxyribose is one of the essential steps in the biosynthesis of DNA. This chemically challenging step is carried out be a number of distinctly different enzyme systems [1]. Each of these systems utilizes a different mechanism for the generation of a transient cysteine-thiyl radical which initiates the reduction of the substrate. Class I enzymes utilize a diferric non-heme iron cluster to generate a stable tyrosine radical [2]. Note that earlier reports of a manganese-based class IV system related to class I in high GC gram positive species was proved to be spurious [3]. Class II enzymes utilize adenosylcobalamin (vitamin B12) [4]. Class III enzymes utilize radical-SAM domain proteins to generate stable glycine radicals [5].
A very small number of genomes appear to be devoid of ribonucleotide reductase sequences, Mycoplasma arthritidis 158L3-1, Mycoplasma bovis Donetta PG45, Ureaplasma urealyticum parvum biovar serovar 3, Borrelia burgdorferi B31 and Borrelia garinii PBi. Each of these is a reduced genome with a limited metabolic portfolio, however other mycoplasma species do contain RNRs. Three possibilities are likely, 1) these genomes harbor a non-orthologous RNR, 2) these genes are located on plasmids or small chromosomes which were lost prior to genomic sequencing (Borrelia, in particular has a number of small chromosomes and plasmids which were sequenced) or 3) these species strictly rely on import of deoxyribonucleic acid from the host environment. |
| Parent Property | GenProp0133: nucleic acid metabolism
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| Literature References | [ 1 ]Kolberg M, Strand KR, Graff P, Andersson KK Structure, function, and mechanism of ribonucleotide reductases. Biochim Biophys Acta 2004 Jun 1;1699(1-2):1-34. PMID 15158709
[ 2 ]Stubbe J Di-iron-tyrosyl radical ribonucleotide reductases. Curr Opin Chem Biol 2003 Apr;7(2):183-8. PMID 12714050
[ 3 ]Hogbom M, Huque Y, Sjoberg BM, Nordlund P Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes. Biochemistry 2002 Jan 29;41(4):1381-9. PMID 11802741
[ 4 ]Lawrence CC, Stubbe J The function of adenosylcobalamin in the mechanism of ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Curr Opin Chem Biol 1998 Oct;2(5):650-5. PMID 9818192
[ 5 ]Fontecave M, Mulliez E, Logan DT Deoxyribonucleotide synthesis in anaerobic microorganisms: the class III ribonucleotide reductase. Prog Nucleic Acid Res Mol Biol 2002;72:95-127. PMID 12206460
[ 6 ]Rodionov DA, Gelfand MS Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling. Trends Genet. 2005 Jul;21(7):385-9. PMID 15949864
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| Web References | Purine metabolism
Pyrimidine metabolism
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| Gene Ontology Term | GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
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| Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
|---|
| class I (aerobic) ribonucleotide reductase: GenProp0289 | I | YES | GenProp0289 (GENPROP): class I (aerobic) ribonucleotide reductase
| GO:0009265: 2'-deoxyribonucleotide biosynthetic process
|
| class II (B12-dependent) ribonucleotide reductase: GenProp0290 | II | YES | GenProp0290 (GENPROP): class II (B12-dependent) ribonucleotide reductase
| GO:0009265: 2'-deoxyribonucleotide biosynthetic process
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| class III (anaerobic) ribonucleotide reductase: GenProp0291 | III | YES | GenProp0291 (GENPROP): class III (anaerobic) ribonucleotide reductase
| GO:0009265: 2'-deoxyribonucleotide biosynthetic process
|
| transcriptional regulator NrdR | NrdR | NO | TIGR00244 (HMM): transcriptional regulator NrdR | GO:0009265: 2'-deoxyribonucleotide biosynthetic process
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