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Escherichia coli K-12 substr. MG1655 Enzyme: 7-cyano-7-deazaguanine reductase



Gene: queF Accession Numbers: G7452 (EcoCyc), b2794, ECK2789

Synonyms: yqcD

Regulation Summary Diagram: ?

Regulation summary diagram for queF

Subunit composition of 7-cyano-7-deazaguanine reductase = [QueF]2
         7-cyano-7-deazaguanine reductase = QueF

Summary:
During biosynthesis of queuosine, QueF catalyzes the formation of preQ1 from preQ0 in an NADPH-dependent reduction [Van05a]. Queuosine is one of the most complex tRNA modifications, occurring at the wobble position of the GUN anticodon in the Asn, Asp, Tyr, and His tRNAs.

QueF has sequence similarity to GTP cyclohydrolase I (FolE), but is missing characteristic zinc-binding and catalytic residues of that enzyme. Both QueF and FolE belong to the tunneling-fold structural superfamily; gel filtration experiments are consistent with a dimeric form of QueF [Van05a].

Locations: cytosol

Map Position: [2,923,370 -> 2,924,218] (63.01 centisomes, 227°)
Length: 849 bp / 282 aa

Molecular Weight of Polypeptide: 32.587 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009162 , DIP:DIP-12848N , EchoBASE:EB2965 , EcoGene:EG13173 , EcoliWiki:b2794 , Mint:MINT-1288325 , OU-Microarray:b2794 , PortEco:queF , PR:PRO_000023670 , Pride:Q46920 , Protein Model Portal:Q46920 , RefSeq:NP_417274 , RegulonDB:G7452 , SMR:Q46920 , String:511145.b2794 , UniProt:Q46920

Relationship Links: InterPro:IN-FAMILY:IPR016428 , InterPro:IN-FAMILY:IPR029139 , InterPro:IN-FAMILY:IPR029500 , Pfam:IN-FAMILY:PF14489 , Pfam:IN-FAMILY:PF14819

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0008616 - queuosine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Van05a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0033739 - preQ1 synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Van05a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046857 - oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for queF 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 ? 25-Feb-2013 by Keseler I , SRI International


Enzymatic reaction of: 7-cyano-7-deazaguanine reductase

EC Number: 1.7.1.13

preQ0 + 2 NADPH + 3 H+ <=> preQ1 + 2 NADP+

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: queuosine biosynthesis

Summary:
None of the tested alternative nitrile substrates acetonitrile, benzonitrile and benzylcyanide were utilized by the enzyme [Moeller13].

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Specific Activity (U/mg)
Citations
preQ0
1.5
0.13, 0.13
0.085, 0.085
58.1
[Moeller13, BRENDA14]
NADPH
6.0
0.14
0.024
[Wilding13, BRENDA14]
NADPH
36.0
0.01
2.8e-4
[Van05a, BRENDA14]
NADPH
0.2
0.0033
0.017
[Moeller13, BRENDA14]

T(opt): 37 °C [BRENDA14, Moeller13]

pH(opt): 7.0 [BRENDA14, Moeller13]


Sequence Features

Protein sequence of 7-cyano-7-deazaguanine reductase with features indicated

Feature Class Location Attached Group Citations Comment
Protein-Segment 88 -> 90  
[UniProt14a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 89  
[Wilding13, UniProt14a]
E → A or L: Drastic decrease in activity.
Nucleotide-Phosphate-Binding-Region 90 -> 91 NADPH
[UniProt15]
UniProt: NADPH.
Mutagenesis-Variant 90  
[Wilding13, UniProt14a]
UniProt: 9-fold decrease in specific activity.
Mutagenesis-Variant 190  
[Wilding13, UniProt14a]
UniProt: Loss of catalytic activity.
Active-Site 190  
[Wilding13, UniProt14a]
UniProt: Thioimide intermediate.
Mutagenesis-Variant 197  
[Wilding13, UniProt14a]
UniProt: Loss of catalytic activity.
Active-Site 197  
[Wilding13, UniProt14a]
UniProt: Proton donor.
Mutagenesis-Variant 228  
[Wilding13, UniProt14a]
UniProt: 11-fold decrease in specific activity.
Mutagenesis-Variant 229  
[Wilding13, UniProt14a]
UniProt: 6.5-fold decrease in specific activity.
Protein-Segment 229 -> 230  
[UniProt14a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 230  
[Wilding13, UniProt14a]
UniProt: 26-fold decrease in specific activity.
Nucleotide-Phosphate-Binding-Region 258 -> 259 NADPH
[UniProt15]
UniProt: NADPH.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

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 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Moeller13: Moeller K, Nguyen GS, Hollmann F, Hanefeld U (2013). "Expression and characterization of the nitrile reductase queF from E. coli." Enzyme Microb Technol 52(3);129-33. PMID: 23410922

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

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-14 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

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

Van05a: Van Lanen SG, Reader JS, Swairjo MA, de Crecy-Lagard V, Lee B, Iwata-Reuyl D (2005). "From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold." Proc Natl Acad Sci U S A 102(12);4264-9. PMID: 15767583

Wilding13: Wilding B, Winkler M, Petschacher B, Kratzer R, Egger S, Steinkellner G, Lyskowski A, Nidetzky B, Gruber K, Klempier N (2013). "Targeting the substrate binding site of E. coli nitrile reductase QueF by modeling, substrate and enzyme engineering." Chemistry 19(22);7007-12. PMID: 23595998

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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 19.0 on Wed May 27, 2015, biocyc13.