Genome Property Definition Page

AccessionGenProp0287
Nameribonucleotide reduction
TypeMETAPATH
DescriptionThe 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 PropertyGenProp0133: nucleic acid metabolism
GenProp0133: nucleic acid metabolism
GenProp0133: nucleic acid metabolism
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
[ 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
[ 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
Web ReferencesPurine metabolism
Pyrimidine metabolism
Purine metabolism
Pyrimidine metabolism
Purine metabolism
Pyrimidine metabolism
Gene Ontology TermGO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)
GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
class I (aerobic) ribonucleotide reductase: GenProp0289IYESGenProp0289 (GENPROP): class I (aerobic) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class I (aerobic) ribonucleotide reductase: GenProp0289IYESGenProp0289 (GENPROP): class I (aerobic) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class I (aerobic) ribonucleotide reductase: GenProp0289IYESGenProp0289 (GENPROP): class I (aerobic) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class II (B12-dependent) ribonucleotide reductase: GenProp0290IIYESGenProp0290 (GENPROP): class II (B12-dependent) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class II (B12-dependent) ribonucleotide reductase: GenProp0290IIYESGenProp0290 (GENPROP): class II (B12-dependent) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class II (B12-dependent) ribonucleotide reductase: GenProp0290IIYESGenProp0290 (GENPROP): class II (B12-dependent) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class III (anaerobic) ribonucleotide reductase: GenProp0291IIIYESGenProp0291 (GENPROP): class III (anaerobic) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class III (anaerobic) ribonucleotide reductase: GenProp0291IIIYESGenProp0291 (GENPROP): class III (anaerobic) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
class III (anaerobic) ribonucleotide reductase: GenProp0291IIIYESGenProp0291 (GENPROP): class III (anaerobic) ribonucleotide reductase
GO:0009265: 2'-deoxyribonucleotide biosynthetic process
transcriptional regulator NrdRNrdRNOTIGR00244 (HMM): transcriptional regulator NrdRGO:0009265: 2'-deoxyribonucleotide biosynthetic process
transcriptional regulator NrdRNrdRNOTIGR00244 (HMM): transcriptional regulator NrdRGO:0009265: 2'-deoxyribonucleotide biosynthetic process
transcriptional regulator NrdRNrdRNOTIGR00244 (HMM): transcriptional regulator NrdRGO:0009265: 2'-deoxyribonucleotide biosynthetic process

Parent Properties
AccessionName
GenProp0133nucleic acid metabolism
GenProp0133nucleic acid metabolism
GenProp0133nucleic acid metabolism

Child Properties
AccessionName
GenProp0289class I (aerobic) ribonucleotide reductase
GenProp0290class II (B12-dependent) ribonucleotide reductase
GenProp0291class III (anaerobic) ribonucleotide reductase
GenProp0289class I (aerobic) ribonucleotide reductase
GenProp0290class II (B12-dependent) ribonucleotide reductase
GenProp0291class III (anaerobic) ribonucleotide reductase
GenProp0289class I (aerobic) ribonucleotide reductase
GenProp0290class II (B12-dependent) ribonucleotide reductase
GenProp0291class III (anaerobic) ribonucleotide reductase

Sibling Properties
AccessionName
GenProp0116DNA metabolism
GenProp0132transcription termination - antitermination Nus factors
GenProp0185nucleotide biosynthesis
GenProp0816nucleoside catabolism/utilization pathways
GenProp0817nucleotide catabolism/utilization pathways
GenProp0819RNA metabolism