Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: 2Fe-2S cluster-containing protein involved in diferric-tyrosyl radical cofactor maintenance



Gene: yfaE Accession Numbers: EG12360 (EcoCyc), b2236, ECK2228

Regulation Summary Diagram: ?

Summary:
YfaE is a [2Fe-2S] cluster-containing protein that is involved in maintenance and possibly in the biosynthesis of active NrdB β2 subunit containing the diferric-tyrosyl radical (Y·) cofactor within ribonucleotide reductase [Wu07a]. YfaE is required for the activity of β during redox stress at high Mn2+ conditions and may provide metal specificity to NrdB [Martin11a].

YfaE was purified from inclusion bodies and refolded/reassembled by addition of Fe2+, Fe3+ and sulfide under anaerobic conditions. The oxidized form of YfaE is not stable and forms aggregates [Wu07a].

Review: [Andrews11]

Citations: [Hristova08]

Gene Citations: [Jordan96]

Locations: cytosol

Map Position: [2,346,536 -> 2,346,790] (50.58 centisomes)
Length: 255 bp / 84 aa

Molecular Weight of Polypeptide: 9.293 kD (from nucleotide sequence), 9.3 kD (experimental) [Wu07a ]

Unification Links: ASAP:ABE-0007390 , EchoBASE:EB2263 , EcoGene:EG12360 , EcoliWiki:b2236 , ModBase:P0ABW3 , OU-Microarray:b2236 , PortEco:yfaE , Protein Model Portal:P0ABW3 , RefSeq:NP_416739 , RegulonDB:EG12360 , SMR:P0ABW3 , String:511145.b2236 , UniProt:P0ABW3

Relationship Links: InterPro:IN-FAMILY:IPR001041 , InterPro:IN-FAMILY:IPR006058 , InterPro:IN-FAMILY:IPR012675 , Pfam:IN-FAMILY:PF00111 , Prosite:IN-FAMILY:PS00197 , Prosite:IN-FAMILY:PS51085

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006124 - ferredoxin metabolic process Inferred from experiment [Hristova08, Wu07a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment Inferred by computational analysis [GOA01a, Wu07a]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Wu07a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Kleinfeld76]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer protein related posttranslational modification

Essentiality data for yfaE 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]

Credits:
Last-Curated ? 11-Mar-2011 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Wu07a]
 
Conserved-Region 2 -> 84
[UniProt09]
UniProt: 2Fe-2S ferredoxin-type;
Metal-Binding-Site 37
[UniProt10]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 42
[UniProt10]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 45
[UniProt10]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 74
[UniProt10]
UniProt: Iron-sulfur (2Fe-2S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b2236 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12360; confirmed by SwissProt match.


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

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

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."

Hristova08: Hristova D, Wu CH, Jiang W, Krebs C, Stubbe J (2008). "Importance of the maintenance pathway in the regulation of the activity of Escherichia coli ribonucleotide reductase." Biochemistry 47(13):3989-99. PMID: 18314964

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

Kleinfeld76: Kleinfeld RG, Morrow H, DeFeo VJ (1976). "Intercellular junctions between decidual cells in the growing deciduoma of the pseudopregnant rat uterus." Biol Reprod 15(5);593-603. PMID: 999999

Martin11a: 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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Wu07a: Wu CH, Jiang W, Krebs C, Stubbe J (2007). "YfaE, a ferredoxin involved in diferric-tyrosyl radical maintenance in Escherichia coli ribonucleotide reductase." Biochemistry 46(41);11577-88. PMID: 17880186

Other References Related to Gene Regulation

Augustin94: Augustin LB, Jacobson BA, Fuchs JA (1994). "Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion." J Bacteriol 1994;176(2);378-87. PMID: 8288532

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

Han98: Han JS, Kwon HS, Yim JB, Hwang DS (1998). "Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli." Mol Gen Genet 259(6);610-4. PMID: 9819053

Hengen97: Hengen PN, Bartram SL, Stewart LE, Schneider TD (1997). "Information analysis of Fis binding sites." Nucleic Acids Res 25(24);4994-5002. PMID: 9396807

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697

Ohtsubo98: Ohtsubo T, Matsuda O, Iba K, Terashima I, Sekiguchi M, Nakabeppu Y (1998). "Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product." Mol Gen Genet 259(6);577-90. PMID: 9819050

Olliver10: Olliver A, Saggioro C, Herrick J, Sclavi B (2010). "DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli." Mol Microbiol 76(6):1555-71. PMID: 20487274

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

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

Tuggle86: Tuggle CK, Fuchs JA (1986). "Regulation of the operon encoding ribonucleotide reductase in Escherichia coli: evidence for both positive and negative control." EMBO J 1986;5(5);1077-85. PMID: 3013616

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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 Sat Dec 20, 2014, biocyc11.