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Escherichia coli K-12 substr. MG1655 Enzyme: ribonucleoside-diphosphate reductase 2

Synonyms: RDPR-II

Subunit composition of ribonucleoside-diphosphate reductase 2 = [(NrdE)2][(NrdF)2]
         ribonucleoside-diphosphate reductase 2, α subunit dimer = (NrdE)2
         ribonucleoside-diphosphate reductase 2, β subunit dimer = (NrdF)2

Summary:
The NrdE and NrdF proteins constitute a second class I ribonucleotide reductase (RDPR-II) in E. coli, converting nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates. The enzyme belongs to the class Ib ribonucleotide reductases that are active under aerobic conditions. Recently, it was shown that RDPR-II is active under conditions of iron starvation, when the housekeeping enzyme RDPR-I (NrdAB) is not active [Martin11].

The catalytic mechanism involves a tyrosyl radical at the active site that inititates ribonucleotide reduction. The nature of the metal ion cofactor for NrdF has been controversial, but recent results show that the MnIII2-Y· form is the active form of NrdF [Cotruvo11, Martin11] and is generated from two HO2- anions supplied by NrdI [Cotruvo10]. Crystal structures of MnII2-NrdF with reduced or oxidized NrdI show a channel connecting the flavin cofactor of NrdI to the NrdF active site [Boal10]. The glutaredoxin-like protein NrdH apparently replaces thioredoxin as the electron donor for ribonucleotide reduction [Gon06].

RDPR-II is an aerobic enzyme that is not essential for growth [Jordan96]. It cannot support aerobic or microaerophilic growth in an nrdAB deletion mutant. However, overexpression of nrdHIEF can rescue the growth defect of the nrdAB mutant [Gon06].

Expression of the nrdHIEF operon is increased by hydroxyurea [Jordan96] and oxidative stress [MonjeCasas01, Martin11]. Expression is highest in minimal medium and in early log phase growth in complex medium; deletion of Trx1 and Grx1 (trxA- grxA-) increases expression more than 100-fold [MonjeCasas01]. nrdHIEF belongs to the Fur regulon [Vassinova00, Martin11]. An nrdEF mutant is viable under both aerobic and anaerobic conditions [Jordan96].

Reviews: [Kolberg04, Reichard10, Sjoberg10, Andrews11]

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009263 - deoxyribonucleotide biosynthetic process Inferred from experiment [Martin11]
Molecular Function: GO:0051063 - CDP reductase activity Inferred from experiment [Cotruvo08]

Credits:
Curated 24-Mar-2008 by Fulcher C , SRI International
Last-Curated ? 11-Mar-2011 by Keseler I , SRI International


Enzymatic reaction of: 2'-deoxycytidine diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase (ribonucleoside-diphosphate reductase 2)

EC Number: 1.17.4.1

CDP + a reduced NrdH glutaredoxin-like protein <=> dCDP + an oxidized NrdH glutaredoxin-like protein + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a reduced NrdH glutaredoxin-like protein: dithiothreitol [Cotruvo08 ]

In Pathways: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)

Summary:
Activity was measured utilizing DTT in place of NrdH [Cotruvo08].


Enzymatic reaction of: 2'-deoxyguanosine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase (ribonucleoside-diphosphate reductase 2)

EC Number: 1.17.4.1

GDP + a reduced NrdH glutaredoxin-like protein <=> dGDP + an oxidized NrdH glutaredoxin-like protein + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , superpathway of guanosine nucleotides de novo biosynthesis II , guanosine deoxyribonucleotides de novo biosynthesis II


Enzymatic reaction of: 2'-deoxyadenosine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase (ribonucleoside-diphosphate reductase 2)

EC Number: 1.17.4.1

ADP + a reduced NrdH glutaredoxin-like protein <=> dADP + an oxidized NrdH glutaredoxin-like protein + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , superpathway of adenosine nucleotides de novo biosynthesis II , adenosine deoxyribonucleotides de novo biosynthesis II


Enzymatic reaction of: 2'-deoxyuridine 5'-diphosphate:oxidized NrdH glutaredoxin-like protein oxidoreductase (ribonucleoside-diphosphate reductase 2)

EC Number: 1.17.4.1

UDP + a reduced NrdH glutaredoxin-like protein <=> dUDP + an oxidized NrdH glutaredoxin-like protein + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)


Enzymatic reaction of: ribonucleoside-diphosphate reductase

EC Number: 1.17.4.1

a reduced thioredoxin + a ribonucleoside diphosphate <=> an oxidized thioredoxin + a 2'-deoxyribonucleoside 5'-diphosphate + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Subunit of ribonucleoside-diphosphate reductase 2: ribonucleoside-diphosphate reductase 2, α subunit dimer

Gene: nrdE Accession Numbers: EG20257 (EcoCyc), b2675, ECK2669

Locations: cytosol

Subunit composition of ribonucleoside-diphosphate reductase 2, α subunit dimer = [NrdE]2

Map Position: [2,799,370 -> 2,801,514] (60.34 centisomes)
Length: 2145 bp / 714 aa

Molecular Weight of Polypeptide: 80.479 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009263 - deoxyribonucleotide biosynthetic process Inferred from experiment [Jordan94]
GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Jordan94]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a]
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred by computational analysis [GOA01, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005971 - ribonucleoside-diphosphate reductase complex Inferred from experiment [Jordan94]
GO:0005737 - cytoplasm Inferred by computational analysis [Jordan94]
GO:0005829 - cytosol

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Unification Links: DIP:DIP-359N , EcoliWiki:b2675 , ModBase:P39452 , PR:PRO_000023405 , Pride:P39452 , Protein Model Portal:P39452 , RefSeq:NP_417161 , SMR:P39452 , String:511145.b2675 , Swiss-Model:P39452 , UniProt:P39452

Relationship Links: InterPro:IN-FAMILY:IPR000788 , InterPro:IN-FAMILY:IPR008926 , InterPro:IN-FAMILY:IPR013346 , InterPro:IN-FAMILY:IPR013509 , InterPro:IN-FAMILY:IPR013554 , InterPro:IN-FAMILY:IPR026459 , Pfam:IN-FAMILY:PF00317 , Pfam:IN-FAMILY:PF02867 , Pfam:IN-FAMILY:PF08343 , Prints:IN-FAMILY:PR01183 , Prosite:IN-FAMILY:PS00089

Gene Citations: [Jordan96]

Essentiality data for nrdE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of ribonucleoside-diphosphate reductase 2: ribonucleoside-diphosphate reductase 2, β subunit dimer

Synonyms: ygaD

Gene: nrdF Accession Numbers: EG12381 (EcoCyc), b2676, ECK2670

Locations: cytosol

Subunit composition of ribonucleoside-diphosphate reductase 2, β subunit dimer = [NrdF]2

Map Position: [2,801,524 -> 2,802,483] (60.38 centisomes)
Length: 960 bp / 319 aa

Molecular Weight of Polypeptide: 36.443 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009263 - deoxyribonucleotide biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Jordan94]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA12, UniProtGOA11a]
GO:0009186 - deoxyribonucleoside diphosphate metabolic process Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Cotruvo10]
GO:0030145 - manganese ion binding Inferred from experiment [Cotruvo11, Cotruvo10]
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred by computational analysis [GOA01]
GO:0005506 - iron ion binding Inferred by computational analysis [Jordan94]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005971 - ribonucleoside-diphosphate reductase complex Inferred from experiment Inferred by computational analysis [GOA01a, Jordan94]
GO:0005737 - cytoplasm Inferred by computational analysis [Jordan94]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Unification Links: DIP:DIP-374N , EcoliWiki:b2676 , ModBase:P37146 , PDB:3N37 , PDB:3N38 , PR:PRO_000023406 , Pride:P37146 , Protein Model Portal:P37146 , RefSeq:NP_417162 , SMR:P37146 , String:511145.b2676 , Swiss-Model:P37146 , UniProt:P37146

Relationship Links: InterPro:IN-FAMILY:IPR000358 , InterPro:IN-FAMILY:IPR009078 , InterPro:IN-FAMILY:IPR012348 , InterPro:IN-FAMILY:IPR026023 , InterPro:IN-FAMILY:IPR026494 , Panther:IN-FAMILY:PTHR23409 , PDB:PART-OF:3N39 , PDB:PART-OF:3N3A , PDB:PART-OF:3N3B , PDB:Structure:4M1F , Pfam:IN-FAMILY:PF00268 , Prosite:IN-FAMILY:PS00368

Gene Citations: [Jordan96]

Essentiality data for nrdF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

References

Andrews11: Andrews SC (2011). "Making DNA without iron - induction of a manganese-dependent ribonucleotide reductase in response to iron starvation." Mol Microbiol 80(2);286-9. PMID: 21371140

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Boal10: Boal AK, Cotruvo JA, Stubbe J, Rosenzweig AC (2010). "Structural basis for activation of class Ib ribonucleotide reductase." Science 329(5998);1526-30. PMID: 20688982

Cotruvo08: Cotruvo JA, Stubbe J (2008). "NrdI, a flavodoxin involved in maintenance of the diferric-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase." Proc Natl Acad Sci U S A 105(38):14383-8. PMID: 18799738

Cotruvo10: Cotruvo JA, Stubbe J (2010). "An active dimanganese(III)-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase." Biochemistry 49(6);1297-309. PMID: 20070127

Cotruvo11: Cotruvo JA, Stubbe J (2011). "Escherichia coli Class Ib Ribonucleotide Reductase Contains a Dimanganese(III)-Tyrosyl Radical Cofactor in Vivo." Biochemistry 50(10);1672-81. PMID: 21250660

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Gon06: Gon S, Faulkner MJ, Beckwith J (2006). "In vivo requirement for glutaredoxins and thioredoxins in the reduction of the ribonucleotide reductases of Escherichia coli." Antioxid Redox Signal 8(5-6);735-42. PMID: 16771665

Jordan94: Jordan A, Pontis E, Atta M, Krook M, Gibert I, Barbe J, Reichard P (1994). "A second class I ribonucleotide reductase in Enterobacteriaceae: characterization of the Salmonella typhimurium enzyme." Proc Natl Acad Sci U S A 1994;91(26);12892-6. PMID: 7809142

Jordan96: Jordan A, Aragall E, Gibert I, Barbe J (1996). "Promoter identification and expression analysis of Salmonella typhimurium and Escherichia coli nrdEF operons encoding one of two class I ribonucleotide reductases present in both bacteria." Mol Microbiol 19(4);777-90. PMID: 8820648

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kolberg04: Kolberg M, Strand KR, Graff P, Andersson KK (2004). "Structure, function, and mechanism of ribonucleotide reductases." Biochim Biophys Acta 1699(1-2);1-34. PMID: 15158709

Martin11: Martin JE, Imlay JA (2011). "The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation." Mol Microbiol 80(2);319-34. PMID: 21338418

MonjeCasas01: Monje-Casas F, Jurado J, Prieto-Alamo MJ, Holmgren A, Pueyo C (2001). "Expression analysis of the nrdHIEF operon from Escherichia coli. Conditions that trigger the transcript level in vivo." J Biol Chem 276(21);18031-7. PMID: 11278973

Reichard10: Reichard P (2010). "Ribonucleotide reductases: substrate specificity by allostery." Biochem Biophys Res Commun 396(1);19-23. PMID: 20494104

Sjoberg10: Sjoberg BM (2010). "Biochemistry. A never-ending story." Science 329(5998);1475-6. PMID: 20847256

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Vassinova00: Vassinova N, Kozyrev D (2000). "A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli." Microbiology 146 Pt 12;3171-82. PMID: 11101675


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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