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Protein

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

Gene

ybjI

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), erythrose 4-phosphate and other phosphoric acid esters (PubMed:15808744, PubMed:16990279, PubMed:24123841).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=70 µM for 5-amino-6-(5-phospho-D-ribitylamino)uracil1 Publication
  2. KM=2.3 mM for FMN (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  3. KM=2.6 mM for Ery4P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  1. Vmax=3 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 sitei9NucleophileBy similarity1
Metal bindingi9MagnesiumBy similarity1
Binding sitei10Phosphate; via amide nitrogenBy similarity1
Metal bindingi11Magnesium; via carbonyl oxygenBy similarity1
Binding sitei192PhosphateBy similarity1
Metal bindingi215MagnesiumBy similarity1
Binding sitei218PhosphateBy similarity1

GO - Molecular functioni

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

GO - Biological processi

  • riboflavin biosynthetic process Source: EcoCyc

Keywordsi

Molecular functionHydrolase
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6442-MONOMER
MetaCyc:G6442-MONOMER
UniPathwayiUPA00275; UER00403

Names & Taxonomyi

Protein namesi
Recommended name:
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI1 Publication (EC:3.1.3.1041 Publication)
Gene namesi
Name:ybjI
Ordered Locus Names:b0844, JW5113
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13678 ybjI

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 YigB.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000544221 – 2715-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjIAdd BLAST271

Proteomic databases

PaxDbiP75809
PRIDEiP75809

Interactioni

Protein-protein interaction databases

BioGridi4262830, 126 interactors
STRINGi316385.ECDH10B_0913

Structurei

3D structure databases

ProteinModelPortaliP75809
SMRiP75809
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni44 – 45Phosphate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108HCJ Bacteria
COG0561 LUCA
HOGENOMiHOG000184782
InParanoidiP75809
KOiK20861
OMAiAPHNNEE
PhylomeDBiP75809

Family and domain databases

Gene3Di3.40.50.1000, 2 hits
InterProiView protein in InterPro
IPR000150 Cof
IPR036412 HAD-like_sf
IPR006379 HAD-SF_hydro_IIB
IPR023214 HAD_sf
SUPFAMiSSF56784 SSF56784, 1 hit
TIGRFAMsiTIGR00099 Cof-subfamily, 1 hit
TIGR01484 HAD-SF-IIB, 1 hit
PROSITEiView protein in PROSITE
PS01229 COF_2, 1 hit

Sequencei

Sequence statusi: Complete.

P75809-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIKLIAVDM DGTFLSDQKT YNRERFMAQY QQMKAQGIRF VVASGNQYYQ
60 70 80 90 100
LISFFPEIAN EIAFVAENGG WVVSEGKDVF NGELSKDAFA TVVEHLLTRP
110 120 130 140 150
EVEIIACGKN SAYTLKKYDD AMKTVAEMYY HRLEYVDNFD NLEDIFFKFG
160 170 180 190 200
LNLSDELIPQ VQKALHEAIG DIMVSVHTGN GSIDLIIPGV HKANGLRQLQ
210 220 230 240 250
KLWGIDDSEV VVFGDGGNDI EMLRQAGFSF AMENAGSAVV AAAKYRAGSN
260 270
NREGVLDVID KVLKHEAPFD Q
Length:271
Mass (Da):30,196
Last modified:May 30, 2000 - v3
Checksum:iAF44E565BCB68BA9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC73931.2
AP009048 Genomic DNA Translation: BAA35548.2
PIRiD64822
RefSeqiNP_415365.4, NC_000913.3
WP_000023565.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73931; AAC73931; b0844
BAA35548; BAA35548; BAA35548
GeneIDi945470
KEGGiecj:JW5113
eco:b0844
PATRICifig|1411691.4.peg.1434

Similar proteinsi

Entry informationi

Entry nameiYBJI_ECOLI
AccessioniPrimary (citable) accession number: P75809
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: March 28, 2018
This is version 130 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health