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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: -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)DescriptionActionsGraphical viewLength
Active sitei16NucleophileBy similarity1
Metal bindingi16MagnesiumBy similarity1
Metal bindingi18MagnesiumBy similarity1
Metal bindingi188MagnesiumBy similarity1

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

Keywordsi

Molecular functionHydrolase
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11202-MONOMER
MetaCyc:EG11202-MONOMER
UniPathwayiUPA00275; UER00403

Names & Taxonomyi

Protein namesi
Recommended name:
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB1 Publication (EC:3.1.3.1041 Publication)
Gene namesi
Name:yigB
Ordered Locus Names:b3812, JW3785
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00001696511 – 2385-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigBAdd BLAST238

Proteomic databases

PaxDbiP0ADP0
PRIDEiP0ADP0

Interactioni

Protein-protein interaction databases

BioGridi4263283, 15 interactors
DIPiDIP-48086N
IntActiP0ADP0, 1 interactor
STRINGi316385.ECDH10B_4004

Structurei

3D structure databases

ProteinModelPortaliP0ADP0
SMRiP0ADP0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni16 – 18Substrate bindingBy similarity3

Sequence similaritiesi

Belongs to the HAD-like hydrolase superfamily.Curated

Phylogenomic databases

eggNOGiENOG4105DFC Bacteria
COG1011 LUCA
HOGENOMiHOG000248345
InParanoidiP0ADP0
KOiK20862
OMAiPQETHDT
PhylomeDBiP0ADP0

Family and domain databases

Gene3Di3.40.50.1000, 2 hits
InterProiView protein in InterPro
IPR036412 HAD-like_sf
IPR006439 HAD-SF_hydro_IA
IPR023214 HAD_sf
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)DescriptionActionsGraphical viewLength
Sequence conflicti13L → V in AAA67608 (PubMed:1379743).Curated1
Sequence conflicti200S → T in AAA24764 (PubMed:2254268).Curated1

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
PATRICifig|1411691.4.peg.2895

Similar proteinsi

Entry informationi

Entry nameiYIGB_ECOLI
AccessioniPrimary (citable) accession number: P0ADP0
Secondary accession number(s): P23306, P76757, Q2M8B8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: March 28, 2018
This is version 92 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health