Escherichia coli K-12 substr. MG1655 Enzyme: 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase

Gene: yigB Accession Numbers: EG11202 (EcoCyc), b3812, ECK3807

Regulation Summary Diagram: ?

Regulation summary diagram for yigB

The identity of the enzyme(s) catalyzing the dephosphorylation of 5-amino-6-(5-phospho-D-ribitylamino)uracil in the riboflavin biosynthesis pathway was long unknown [Harzer78, Neidhardt96]. [Haase13] have now shown that at least two enzymes, YigB and YbjI, can catalyze this reaction.

YigB was initially identified as an FMN phosphatase that belongs to the superfamily of haloacid dehalogenase (HAD)-like hydrolases [Kuznetsova06].

yigB is important for formation of dormant persister cells; overexpression of yigB leads to increased tolerance to ofloxacin [Hansen08]. Deletion of yigB alone does not result in riboflavin auxotrophy [Baba06].

Locations: cytosol

Map Position: [3,995,206 -> 3,995,922] (86.11 centisomes, 310°)
Length: 717 bp / 238 aa

Molecular Weight of Polypeptide: 27.122 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012450 , DIP:DIP-48086N , EchoBASE:EB1187 , EcoGene:EG11202 , EcoliWiki:b3812 , ModBase:P0ADP0 , OU-Microarray:b3812 , PortEco:yigB , Protein Model Portal:P0ADP0 , RefSeq:NP_418257 , RegulonDB:EG11202 , SMR:P0ADP0 , String:511145.b3812 , UniProt:P0ADP0

Relationship Links: InterPro:IN-FAMILY:IPR006439 , InterPro:IN-FAMILY:IPR023214 , Pfam:IN-FAMILY:PF00702

In Paralogous Gene Group: 276 (8 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009231 - riboflavin biosynthetic process Inferred from experiment [Haase13]
GO:0016311 - dephosphorylation Inferred from experiment [Haase13, Kuznetsova06]
GO:0022611 - dormancy process Inferred from experiment [Hansen08]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Kuznetsova06]
GO:0016791 - phosphatase activity Inferred from experiment [Kuznetsova06]
GO:0043726 - 5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity Inferred from experiment [Haase13]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers riboflavin

Essentiality data for yigB 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]

Last-Curated ? 21-Oct-2013 by Keseler I , SRI International

Enzymatic reaction of: 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase

5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O <=> 5-amino-6-(D-ribitylamino)uracil + phosphate

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.

The reaction is favored in the direction shown.

In Pathways: flavin biosynthesis I (bacteria and plants)

Cofactors or Prosthetic Groups: Mg2+

Kinetic Parameters:

Km (μM)

Enzymatic reaction of: FMN phosphatase (5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase)

Synonyms: HAD7

EC Number: 3.1.3.-

FMN + H2O <=> riboflavin + phosphate

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.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 13
[Daniels92, UniProt10]
UniProt: (in Ref. 2; AAA67608);
Metal-Binding-Site 16
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Active-Site 16
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity.
Protein-Segment 16 -> 18
UniProt: Substrate; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 18
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 188
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 200
[Colloms90, UniProt10]
UniProt: (in Ref. 1; AAA24764);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 b3812 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11202; confirmed by SwissProt match.


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

Colloms90: Colloms SD, Sykora P, Szatmari G, Sherratt DJ (1990). "Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases." J Bacteriol 172(12);6973-80. PMID: 2254268

Daniels92: Daniels DL, Plunkett G, Burland V, Blattner FR (1992). "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Science 1992;257(5071);771-8. PMID: 1379743

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

Haase13: Haase I, Sarge S, Illarionov B, Laudert D, Hohmann HP, Bacher A, Fischer M (2013). "Enzymes from the haloacid dehalogenase (HAD) superfamily catalyse the elusive dephosphorylation step of riboflavin biosynthesis." Chembiochem 14(17);2272-5. PMID: 24123841

Hansen08: Hansen S, Lewis K, Vulic M (2008). "Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli." Antimicrob Agents Chemother 52(8);2718-26. PMID: 18519731

Harzer78: Harzer G, Rokos H, Otto MK, Bacher A, Ghisla S (1978). "Biosynthesis of riboflavin. 6,7-Dimethyl-8-ribityllumazine 5'-phosphate is not a substrate for riboflavin synthase." Biochim Biophys Acta 540(1);48-54. PMID: 416855

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

Kuznetsova06: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF (2006). "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." J Biol Chem 281(47):36149-61. PMID: 16990279

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 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

Richaud88: Richaud C, Printz C (1988). "Nucleotide sequence of the dapF gene and flanking regions from Escherichia coli K12." Nucleic Acids Res 16(21);10367. PMID: 3057443

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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 Oct 7, 2015, biocyc14.