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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: 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), 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
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6442-MONOMER.
ECOL316407:JW5113-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.-1 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.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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. 120 interactors.
STRINGi511145.b0844.

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.
OMAiLNDIFFK.
PhylomeDBiP75809.

Family and domain databases

Gene3Di3.40.50.1000. 2 hits.
InterProiIPR023214. HAD-like_dom.
IPR006379. HAD-SF_hydro_IIB.
IPR000150. Hypothet_cof.
[Graphical view]
PfamiPF08282. Hydrolase_3. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR00099. Cof-subfamily. 1 hit.
TIGR01484. HAD-SF-IIB. 1 hit.
PROSITEiPS01229. COF_2. 1 hit.
[Graphical view]

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.
PATRICi32116893. VBIEscCol129921_0872.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP75809.
SMRiP75809.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262830. 120 interactors.
STRINGi511145.b0844.

Proteomic databases

PaxDbiP75809.
PRIDEiP75809.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73931; AAC73931; b0844.
BAA35548; BAA35548; BAA35548.
GeneIDi945470.
KEGGiecj:JW5113.
eco:b0844.
PATRICi32116893. VBIEscCol129921_0872.

Organism-specific databases

EchoBASEiEB3442.
EcoGeneiEG13678. ybjI.

Phylogenomic databases

eggNOGiENOG4108HCJ. Bacteria.
COG0561. LUCA.
HOGENOMiHOG000184782.
InParanoidiP75809.
OMAiLNDIFFK.
PhylomeDBiP75809.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00403.
BioCyciEcoCyc:G6442-MONOMER.
ECOL316407:JW5113-MONOMER.
MetaCyc:G6442-MONOMER.

Miscellaneous databases

PROiP75809.

Family and domain databases

Gene3Di3.40.50.1000. 2 hits.
InterProiIPR023214. HAD-like_dom.
IPR006379. HAD-SF_hydro_IIB.
IPR000150. Hypothet_cof.
[Graphical view]
PfamiPF08282. Hydrolase_3. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR00099. Cof-subfamily. 1 hit.
TIGR01484. HAD-SF-IIB. 1 hit.
PROSITEiPS01229. COF_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYBJI_ECOLI
AccessioniPrimary (citable) accession number: P75809
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 121 of the entry and version 3 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.