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



Gene: nrdG Accession Numbers: G812 (EcoCyc), b4237, ECK4232

Synonyms: yjgE

Regulation Summary Diagram: ?

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

Subunit composition of ribonucleoside triphosphate reductase activase = [NrdG]2

Summary:
An nrdG 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].

The NrdG activase activates the NrdD reductase under anaerobic conditions.

Using site-directed mutagenesis, the participation of three cysteine residues in iron chelation in the (4Fe-4S) cluster of this enzyme was demonstrated, but a fourth ligand remained unidentified [Tamarit00].

Citations: [Fontecave02]

Gene Citations: [Zaslaver06]

Locations: cytosol

Map Position: [4,457,923 <- 4,458,387] (96.08 centisomes)
Length: 465 bp / 154 aa

Molecular Weight of Polypeptide: 17.446 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013860 , DIP:DIP-48068N , EchoBASE:EB2414 , EcoGene:EG12523 , EcoliWiki:b4237 , OU-Microarray:b4237 , PortEco:nrdG , PR:PRO_000023407 , Protein Model Portal:P0A9N8 , RefSeq:NP_418658 , RegulonDB:G812 , SMR:P0A9N8 , String:511145.b4237 , UniProt:P0A9N8

Relationship Links: InterPro:IN-FAMILY:IPR001989 , InterPro:IN-FAMILY:IPR012837 , InterPro:IN-FAMILY:IPR013785 , Prosite:IN-FAMILY:PS01087

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Garriga96]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0051536 - iron-sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Mulliez93]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Tamarit99]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0043365 - [formate-C-acetyltransferase]-activating enzyme activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0031250 - anaerobic ribonucleoside-triphosphate reductase complex Inferred from experiment [Garriga96]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer protein related posttranslational modification
metabolism central intermediary metabolism nucleotide and nucleoside conversions
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for nrdG 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 ? 24-Mar-2008 by Fulcher C , SRI International


Enzymatic reaction of: ribonucleoside triphosphate reductase activase

EC Number: 1.97.1.-

S-adenosyl-L-methionine + an inactive ribonucleoside triphosphate reductase <=> 5'-deoxyadenosine + an active ribonucleoside triphosphate reductase + L-methionine

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

This reaction is reversible.

Summary:
The activase forms a multi-enzyme complex with flavodoxin-NADP reductase, S-adenosylmethionine (AdoMet) and the anaerobic ribonucleoside triphosphate reductase itself. The activase contains a 4Fe-4S cluster which is reduced by flavodoxin. AdoMet binds to the activase and is in turn reduced to a radical intermediate. The intermediate is cleaved to a 5'-deoxyadenosyl radical and methionine. The 5'-deoxyadenosyl radical generates an essential glycyl radical at Gly681 of anaerobic ribonucleoside triphosphate reductase by abstracting a hydrogen atom. The mechanism is analogous to pyruvate formate-lyase activating enzyme. [Bianchi93, Wong93, Sun95, Ollagnier97, Tamarit99]

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Tamarit99]


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
Metal-Binding-Site 26
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: probable;
Metal-Binding-Site 30
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: probable;
Metal-Binding-Site 33
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: probable;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4237 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene G812.


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

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

Fontecave02: Fontecave M, Mulliez E, Logan DT (2002). "Deoxyribonucleotide synthesis in anaerobic microorganisms: the class III ribonucleotide reductase." Prog Nucleic Acid Res Mol Biol 2002;72;95-127. PMID: 12206460

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

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

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

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

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

Tamarit00: Tamarit J, Gerez C, Meier C, Mulliez E, Trautwein A, Fontecave M (2000). "The activating component of the anaerobic ribonucleotide reductase from Escherichia coli. An iron-sulfur center with only three cysteines." J Biol Chem 275(21);15669-75. PMID: 10821845

Tamarit99: Tamarit J, Mulliez E, Meier C, Trautwein A, Fontecave M (1999). "The anaerobic ribonucleotide reductase from Escherichia coli. The small protein is an activating enzyme containing a [4fe-4s](2+) center." J Biol Chem 1999;274(44);31291-6. PMID: 10531327

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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

Wong93: Wong KK, Murray BW, Lewisch SA, Baxter MK, Ridky TW, Ulissi-DeMario L, Kozarich JW (1993). "Molecular properties of pyruvate formate-lyase activating enzyme." Biochemistry 1993;32(51);14102-10. PMID: 8260492

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, BIOCYC14A.