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BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Enzyme: putative nucleoside (IDP) diphosphatase



Gene: yibQ Accession Numbers: EG12298 (EcoCyc), b3614, ECK3604

Regulation Summary Diagram: ?

Summary:
Based on sequence similarity, YibQ is predicted to be a nucleoside (IDP) diphosphatase [Reed03].

Map Position: [3,786,124 -> 3,787,083] (81.6 centisomes)
Length: 960 bp / 319 aa

Molecular Weight of Polypeptide: 35.353 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011824 , EchoBASE:EB2206 , EcoGene:EG12298 , EcoliWiki:b3614 , OU-Microarray:b3614 , PortEco:yibQ , Protein Model Portal:P37691 , RefSeq:NP_418071 , RegulonDB:EG12298 , SMR:P37691 , String:511145.b3614 , UniProt:P37691

Relationship Links: InterPro:IN-FAMILY:IPR002509 , InterPro:IN-FAMILY:IPR006837 , InterPro:IN-FAMILY:IPR011330 , Pfam:IN-FAMILY:PF04748

Gene-Reaction Schematic: ?

Instance reactions of [a nucleoside diphosphate + H2O → a nucleoside 5'-monophosphate + phosphate + H+] (3.6.1.6):
i1: GDP + H2O → GMP + phosphate + H+ (3.6.1.42)

i2: UDP + H2O → UMP + phosphate + H+ (3.6.1.6)

i3: CDP + H2O → CMP + phosphate + H+ (3.6.1.6)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01a]

MultiFun Terms: metabolism

Essentiality data for yibQ 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]

Enzymatic reaction of: putative nucleoside (IDP) diphosphatase

Synonyms: nucleoside-diphosphatase, nucleoside-diphosphate phosphohydrolase

EC Number: 3.6.1.6

a nucleoside diphosphate + H2O <=> a nucleoside 5'-monophosphate + phosphate + H+

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.


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Chain 24 -> 319
[UniProt09]
UniProt: Uncharacterized protein yibQ;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
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 b3614 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12298; 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

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

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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.

Other References Related to Gene Regulation

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

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

Shimada11: Shimada T, Yamamoto K, Ishihama A (2011). "Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli." J Bacteriol 193(3);649-59. PMID: 21115656


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, BIOCYC14A.