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



Gene: nrdD Accession Numbers: EG11417 (EcoCyc), b4238, ECK4233

Regulation Summary Diagram: ?

Component of: anaerobic nucleoside-triphosphate reductase activating system (summary available)

Subunit composition of ribonucleoside-triphosphate reductase = [NrdD]2
         ribonucleoside-triphosphate reductase = NrdD

Alternative forms of ribonucleoside-triphosphate reductase: oxidized ribonucleoside-triphosphate reductase

Summary:
The NrdD reductase is activated by the NrdG activase under anaerobic conditions and is inactivated by oxygen. The protein is highly sensitive to O2.

An nrdD null mutant does not grow under entirely anaerobic conditions, but grows under aerobic or microaerophilic conditions due to the activity of NrdA and/or NrdB [Garriga96].

Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB), class Ib (encoded by nrdE and nrdF) and class III (encoded by nrdD) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction. Regeneration of the enzymes is accomplished by corresponding reductive enzyme systems [Gon06] and discussed in [Torrents07].

This enzyme is a class III ribonucleotide reductase that is essential for anaerobic growth. In E. coli strain DHB4, construction of deletion mutants and analysis of their growth characteristics showed that the main ribonucleotide reductase activity in strict anaerobiosis is provided by the products of genes nrdD and nrdG. Under highly restricted oxygen condtions, the products of genes nrdA and nrdB can support some growth in a strain containing a deletion of nrdD and nrdG. Either thioredoxin reductase or glutathione reductase are required for anaerobic growth, suggesting that these reductive pathways contribute to enzyme activity [Gon06].

Locations: cytosol

Map Position: [4,458,545 <- 4,460,683] (96.1 centisomes)
Length: 2139 bp / 712 aa

Molecular Weight of Polypeptide: 80.023 kD (from nucleotide sequence)

pI: 6.87

Unification Links: ASAP:ABE-0013865 , CGSC:34589 , DIP:DIP-10358N , EchoBASE:EB1388 , EcoGene:EG11417 , EcoliWiki:b4238 , ModBase:P28903 , OU-Microarray:b4238 , PortEco:nrdD , Pride:P28903 , Protein Model Portal:P28903 , RefSeq:NP_418659 , RegulonDB:EG11417 , SMR:P28903 , String:511145.b4238 , Swiss-Model:P28903 , UniProt:P28903

Relationship Links: InterPro:IN-FAMILY:IPR001150 , InterPro:IN-FAMILY:IPR005144 , InterPro:IN-FAMILY:IPR012833 , InterPro:IN-FAMILY:IPR019777 , Pfam:IN-FAMILY:PF03477 , Prosite:IN-FAMILY:PS00850 , Prosite:IN-FAMILY:PS51149 , Prosite:IN-FAMILY:PS51161

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Garriga96]
GO:0006260 - DNA replication Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Luttringer09]
GO:0008998 - ribonucleoside-triphosphate reductase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Eliasson94]
GO:0042803 - protein homodimerization activity Inferred from experiment [Eliasson92]
GO:0051065 - CTP reductase activity Inferred from experiment [Eliasson92]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0031250 - anaerobic ribonucleoside-triphosphate reductase complex Inferred from experiment [Garriga96]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism 2'-deoxyribonucleotide metabolism

Essentiality data for nrdD 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]

Credits:
Last-Curated ? 21-Dec-2011 by Fulcher C , SRI International


Enzymatic reaction of: ATP reductase (ribonucleoside-triphosphate reductase)

EC Number: 1.17.4.2

dATP + an oxidized flavodoxin + H2O <=> ATP + a reduced flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the opposite direction.

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

Summary:


Enzymatic reaction of: GTP reductase (ribonucleoside-triphosphate reductase)

EC Number: 1.17.4.2

dGTP + an oxidized flavodoxin + H2O <=> GTP + a reduced flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the opposite direction.

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: UTP reductase (ribonucleoside-triphosphate reductase)

EC Number: 1.17.4.2

dUTP + an oxidized flavodoxin + H2O <=> UTP + a reduced flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the opposite direction.

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


Enzymatic reaction of: CTP reductase (ribonucleoside-triphosphate reductase)

EC Number: 1.17.4.2

dCTP + an oxidized flavodoxin + H2O <=> CTP + a reduced flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the opposite direction.

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


Enzymatic reaction of: ribonucleoside-triphosphate reductase

Synonyms: ribonucleotide reductase, anaerobic ribonucleoside-triphosphate reductase

a reduced flavodoxin + a ribonucleoside triphosphate <=> an oxidized flavodoxin + a deoxyribonucleoside triphosphate + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

Alternative Substrates [Comment 5]:

Summary:
The reductase has the ability to reduce the four common ribonucleoside triphosphates. Each substrate requires the presence of a specific effector for its reduction [Eliasson94].

Cofactors or Prosthetic Groups: Zn2+ [Luttringer09], [FeS] iron-sulfur cluster [Comment 6, Mulliez93, Ollagnier97], K+ [Eliasson92], Mg2+ [Eliasson92]

Activators (Allosteric): dTTP [Eliasson94, Comment 7] , ATP [Eliasson94, Comment 8] , dGTP [Eliasson94, Comment 9]

Inhibitors (Unknown Mechanism): Co2+ [Eliasson92] , Fe2+ [Eliasson92] , 2'-chloro-dCTP [Eliasson94a] , 2'-azido-dCTP [Eliasson94a] , 2-fluoro-dCTP [Eliasson94a] , EDTA [Eliasson92] , S-adenosyl-L-homocysteine [Eliasson92] , K+ [Eliasson92, Comment 10] , Mg2+ [Eliasson92, Comment 11] , dithiothreitol [Eliasson92, Comment 11] , dATP [Eliasson94] , dGTP [Eliasson94, Comment 12] , dTTP [Eliasson94, Comment 13]

Primary Physiological Regulators of Enzyme Activity: ATP , dGTP , dTTP


Subunit of: anaerobic nucleoside-triphosphate reductase activating system

Subunit composition of anaerobic nucleoside-triphosphate reductase activating system = [(NrdD)2][(NrdG)2][Fpr]
         ribonucleoside-triphosphate reductase = (NrdD)2
                 ribonucleoside-triphosphate reductase = NrdD
         ribonucleoside triphosphate reductase activase = (NrdG)2
         flavodoxin NADP+ reductase = Fpr (summary available)

Summary:
The anaerobic nucleoside-triphosphate reductase activating system is composed of three enzymes and several compounds. Anaerobic nucleoside-triphosphate reductase is activated through the action of a specific activating enzyme, nucleoside-triphosphate reductase activase, flavodoxin NADP+ reductase, S-adenosylmethionine, flavodoxin and NADPH. All of these components form a multi-enzyme complex with the ribonucleoside reductase itself. [Bianchi93, Sun95]

Credits:
Last-Curated ? 24-Mar-2008 by Fulcher C , SRI International


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 3 -> 92
[UniProt09]
UniProt: ATP-cone;
Sequence-Conflict 257
[Sun93, UniProt09]
Alternate sequence: G → R; UniProt: (in Ref. 1; AAA24226); Non-Experimental Qualifier: variant;
Alternate sequence: G → missing; UniProt: (in Ref. 1; AAA24226);
Sequence-Conflict 420
[Sun93, UniProt09]
Alternate sequence: A → P; UniProt: (in Ref. 1; AAA24226); Non-Experimental Qualifier: variant;
Alternate sequence: A → missing; UniProt: (in Ref. 1; AAA24226);
Conserved-Region 583 -> 708
[UniProt09]
UniProt: Glycine radical;
Metal-Binding-Site 644
[UniProt08]
UniProt: Zinc;
Metal-Binding-Site 647
[UniProt08]
UniProt: Zinc;
Metal-Binding-Site 662
[UniProt08]
UniProt: Zinc;
Metal-Binding-Site 665
[UniProt08]
UniProt: Zinc;
Glycyl-Radical-Modification 681
[UniProt12a]
UniProt: Glycine radical; Non-Experimental Qualifier: by similarity.
Modified-Residue 681
[UniProt09]
UniProt: Glycine radical;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4238 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11417; confirmed by SwissProt match.


References

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

Bianchi93: Bianchi V, Reichard P, Eliasson R, Pontis E, Krook M, Jornvall H, Haggard-Ljungquist E (1993). "Escherichia coli ferredoxin NADP+ reductase: activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr), and overexpression of the protein." J Bacteriol 1993;175(6);1590-5. PMID: 8449868

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

Eliasson92: Eliasson R, Pontis E, Fontecave M, Gerez C, Harder J, Jornvall H, Krook M, Reichard P (1992). "Characterization of components of the anaerobic ribonucleotide reductase system from Escherichia coli." J Biol Chem 267(35);25541-7. PMID: 1460049

Eliasson94: Eliasson R, Pontis E, Sun X, Reichard P (1994). "Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli." J Biol Chem 269(42);26052-7. PMID: 7929317

Eliasson94a: Eliasson R, Pontis E, Eckstein F, Reichard P (1994). "Interactions of 2'-modified azido- and haloanalogs of deoxycytidine 5'-triphosphate with the anaerobic ribonucleotide reductase of Escherichia coli." J Biol Chem 1994;269(42);26116-20. PMID: 7929323

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

Garriga96: Garriga X, Eliasson R, Torrents E, Jordan A, Barbe J, Gibert I, Reichard P (1996). "nrdD and nrdG genes are essential for strict anaerobic growth of Escherichia coli." Biochem Biophys Res Commun 1996;229(1);189-92. PMID: 8954104

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

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

Luttringer09: Luttringer F, Mulliez E, Dublet B, Lemaire D, Fontecave M (2009). "The Zn center of the anaerobic ribonucleotide reductase from E. coli." J Biol Inorg Chem 14(6);923-33. PMID: 19381696

Mulliez93: Mulliez E, Fontecave M, Gaillard J, Reichard P (1993). "An iron-sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli." J Biol Chem 1993;268(4);2296-9. PMID: 8381402

Ollagnier97: Ollagnier S, Mulliez E, Schmidt PP, Eliasson R, Gaillard J, Deronzier C, Bergman T, Graslund A, Reichard P, Fontecave M (1997). "Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction." J Biol Chem 1997;272(39);24216-23. PMID: 9305874

Sun93: Sun X, Harder J, Krook M, Jornvall H, Sjoberg BM, Reichard P (1993). "A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene." Proc Natl Acad Sci U S A 90(2);577-81. PMID: 8421692

Sun95: Sun X, Eliasson R, Pontis E, Andersson J, Buist G, Sjoberg BM, Reichard P (1995). "Generation of the glycyl radical of the anaerobic Escherichia coli ribonucleotide reductase requires a specific activating enzyme." J Biol Chem 1995;270(6);2443-6. PMID: 7852304

Torrents07: Torrents E, Grinberg I, Gorovitz-Harris B, Lundstrom H, Borovok I, Aharonowitz Y, Sjoberg BM, Cohen G (2007). "NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes." J Bacteriol 189(14);5012-21. PMID: 17496099

UniProt08: UniProt Consortium (2008). "UniProt version 14.6 released on 2008-12-16." Database.

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Boston03: Boston T, Atlung T (2003). "FNR-mediated oxygen-responsive regulation of the nrdDG operon of Escherichia coli." J Bacteriol 185(17);5310-3. PMID: 12923108

Cendra13: Cendra Mdel M, Juarez A, Madrid C, Torrents E (2013). "H-NS is a novel transcriptional modulator of the ribonucleotide reductase genes in Escherichia coli." J Bacteriol 195(18);4255-63. PMID: 23873909

Roca08: Roca I, Ballana E, Panosa A, Torrents E, Gibert I (2008). "Fumarate and nitrate reduction (FNR) dependent activation of the Escherichia coli anaerobic ribonucleotide reductase nrdDG promoter." Int Microbiol 11(1);49-56. PMID: 18683632


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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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