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Protein

5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB

Gene

yigB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dephosphorylation of 5-amino-6-(5-phospho-D-ribitylamino)uracil, and thus could be involved in the riboflavin biosynthesis pathway (PubMed:24123841). Is also able to dephosphorylate flavin mononucleotide (FMN) and other phosphoric acid esters (PubMed:16990279) (PubMed:24123841). YigB is important for the formation of dormant persister cells (PubMed:18519731).3 Publications

Catalytic activityi

5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-(D-ribitylamino)uracil + phosphate.1 Publication

Cofactori

Mg2+1 Publication, Mn2+1 Publication, Co2+1 Publication, Zn2+1 PublicationNote: Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.1 Publication

Kineticsi

  1. KM=20 µM for 5-amino-6-(5-phospho-D-ribitylamino)uracil1 Publication
  2. KM=1 mM for FMN (with magnesium ions as cofactor and at pH 9)1 Publication
  1. Vmax=4 µmol/min/mg enzyme with 5-amino-6-(5-phospho-D-ribitylamino)uracil as substrate1 Publication

pH dependencei

Optimum pH is 6-7.5.1 Publication

Pathwayi: riboflavin biosynthesis

This protein is involved in step 4 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.1 Publication
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. GTP cyclohydrolase-2 (ribA)
  2. Riboflavin biosynthesis protein RibD (ribD)
  3. Riboflavin biosynthesis protein RibD (ribD)
  4. 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI (ybjI), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB (yigB)
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei16 – 161NucleophileBy similarity
Metal bindingi16 – 161MagnesiumBy similarity
Metal bindingi18 – 181MagnesiumBy similarity
Metal bindingi188 – 1881MagnesiumBy similarity

GO - Molecular functioni

  • 5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity Source: EcoCyc
  • magnesium ion binding Source: UniProtKB
  • phosphatase activity Source: EcoCyc

GO - Biological processi

  • dormancy process Source: EcoCyc
  • riboflavin biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11202-MONOMER.
ECOL316407:JW3785-MONOMER.
MetaCyc:EG11202-MONOMER.
UniPathwayiUPA00275; UER00403.

Names & Taxonomyi

Protein namesi
Recommended name:
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB1 Publication (EC:3.1.3.-1 Publication)
Gene namesi
Name:yigB
Ordered Locus Names:b3812, JW3785
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11202. yigB.

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene can grow in the absence of exogenous riboflavin; this may be due to the presence of the functionally redundant protein YbjI.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2382385-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigBPRO_0000169651Add
BLAST

Proteomic databases

PaxDbiP0ADP0.

Interactioni

Protein-protein interaction databases

BioGridi4263283. 13 interactions.
DIPiDIP-48086N.
STRINGi511145.b3812.

Structurei

3D structure databases

ProteinModelPortaliP0ADP0.
SMRiP0ADP0. Positions 10-238.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni16 – 183Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the HAD-like hydrolase superfamily.Curated

Phylogenomic databases

eggNOGiENOG4105DFC. Bacteria.
COG1011. LUCA.
HOGENOMiHOG000248345.
InParanoidiP0ADP0.
KOiK07025.
OMAiYHPALRD.
OrthoDBiEOG6W19QD.
PhylomeDBiP0ADP0.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR006439. HAD-SF_hydro_IA.
[Graphical view]
PfamiPF13419. HAD_2. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01549. HAD-SF-IA-v1. 1 hit.

Sequencei

Sequence statusi: Complete.

P0ADP0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFYRPLGRI SALTFDLDDT LYDNRPVILR TEREALTFVQ NYHPALRSFQ
60 70 80 90 100
NEDLQRLRQA VREAEPEIYH DVTRWRFRSI EQAMLDAGLS AEEASAGAHA
110 120 130 140 150
AMINFAKWRS RIDVPQQTHD TLKQLAKKWP LVAITNGNAQ PELFGLGDYF
160 170 180 190 200
EFVLRAGPHG RSKPFSDMYF LAAEKLNVPI GEILHVGDDL TTDVGGAIRS
210 220 230
GMQACWIRPE NGDLMQTWDS RLLPHLEISR LASLTSLI
Length:238
Mass (Da):27,122
Last modified:December 6, 2005 - v1
Checksum:i9C1BDE710641E0D6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti13 – 131L → V in AAA67608 (PubMed:1379743).Curated
Sequence conflicti200 – 2001S → T in AAA24764 (PubMed:2254268).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M38257 Genomic DNA. Translation: AAA24764.1.
M87049 Genomic DNA. Translation: AAA67608.1.
U00096 Genomic DNA. Translation: AAC76815.1.
AP009048 Genomic DNA. Translation: BAE77488.1.
X00738 Genomic DNA. No translation available.
PIRiD37841.
RefSeqiNP_418257.1. NC_000913.3.
WP_001213584.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76815; AAC76815; b3812.
BAE77488; BAE77488; BAE77488.
GeneIDi948357.
KEGGiecj:JW3785.
eco:b3812.
PATRICi32123125. VBIEscCol129921_3928.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M38257 Genomic DNA. Translation: AAA24764.1.
M87049 Genomic DNA. Translation: AAA67608.1.
U00096 Genomic DNA. Translation: AAC76815.1.
AP009048 Genomic DNA. Translation: BAE77488.1.
X00738 Genomic DNA. No translation available.
PIRiD37841.
RefSeqiNP_418257.1. NC_000913.3.
WP_001213584.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0ADP0.
SMRiP0ADP0. Positions 10-238.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263283. 13 interactions.
DIPiDIP-48086N.
STRINGi511145.b3812.

Proteomic databases

PaxDbiP0ADP0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76815; AAC76815; b3812.
BAE77488; BAE77488; BAE77488.
GeneIDi948357.
KEGGiecj:JW3785.
eco:b3812.
PATRICi32123125. VBIEscCol129921_3928.

Organism-specific databases

EchoBASEiEB1187.
EcoGeneiEG11202. yigB.

Phylogenomic databases

eggNOGiENOG4105DFC. Bacteria.
COG1011. LUCA.
HOGENOMiHOG000248345.
InParanoidiP0ADP0.
KOiK07025.
OMAiYHPALRD.
OrthoDBiEOG6W19QD.
PhylomeDBiP0ADP0.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00403.
BioCyciEcoCyc:EG11202-MONOMER.
ECOL316407:JW3785-MONOMER.
MetaCyc:EG11202-MONOMER.

Miscellaneous databases

PROiP0ADP0.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR006439. HAD-SF_hydro_IA.
[Graphical view]
PfamiPF13419. HAD_2. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01549. HAD-SF-IA-v1. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases."
    Colloms S.D., Sykora P., Szatmari G., Sherratt D.J.
    J. Bacteriol. 172:6973-6980(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
    Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
    Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 13.
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "The nucleotide sequence of the uvrD gene of E. coli."
    Finch P.W., Emmerson P.T.
    Nucleic Acids Res. 12:5789-5799(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 183-238.
  6. "Transcription of the uvrD gene of Escherichia coli is controlled by the lexA repressor and by attenuation."
    Easton A.M., Kushner S.R.
    Nucleic Acids Res. 11:8625-8640(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 183-238.
  7. "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family."
    Kuznetsova E., Proudfoot M., Gonzalez C.F., Brown G., Omelchenko M.V., Borozan I., Carmel L., Wolf Y.I., Mori H., Savchenko A.V., Arrowsmith C.H., Koonin E.V., Edwards A.M., Yakunin A.F.
    J. Biol. Chem. 281:36149-36161(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A PHOSPHATASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.
  8. "Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli."
    Hansen S., Lewis K., Vulic M.
    Antimicrob. Agents Chemother. 52:2718-2726(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN THE FORMATION OF DORMANT PERSISTER CELLS.
  9. "Enzymes from the haloacid dehalogenase (HAD) superfamily catalyse the elusive dephosphorylation step of riboflavin biosynthesis."
    Haase I., Sarge S., Illarionov B., Laudert D., Hohmann H.P., Bacher A., Fischer M.
    ChemBioChem 14:2272-2275(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE, PATHWAY.

Entry informationi

Entry nameiYIGB_ECOLI
AccessioniPrimary (citable) accession number: P0ADP0
Secondary accession number(s): P23306, P76757, Q2M8B8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: July 6, 2016
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.