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Protein

Sugar phosphatase YbiV

Gene

ybiV

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

Functioni

Catalyzes the hydrolysis of sugar phosphate to sugar and inorganic phosphate. Has a wide substrate specificity catalyzing the hydrolysis of ribose-5-phosphate, glucose-6-phosphate, fructose-1-phosphate, acetyl-phosphate, glycerol-1-phosphate, glycerol-2-phosphate, 2-deoxy-glucose-6-phosphate, mannose-6-phosphate and fructose-6-phosphate. Appears to have a low level of phosphotransferase activity using monophosphates as the phosphate donor.3 Publications

Catalytic activityi

Sugar phosphate + H2O = sugar + 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

Glucose-6-phosphate is also a good substrate with a relative activity of 62.5% versus the activity with ribose-5-phosphate.

  1. KM=0.12 mM for imido-di-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  2. KM=1.4 mM for fructose-1-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  3. KM=2.4 mM for ribose-5-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  4. KM=3.1 mM for glucose-6-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  5. KM=4.9 mM for acetyl-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  6. KM=6 mM for ribose-5-phosphate (at pH 5.4)2 Publications
  7. KM=6 mM for glycerol-1-phosphate (at pH 5.4)2 Publications
  8. KM=4.5 mM for glycerol-2-phosphate (at pH 5.4)2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei9 – 91NucleophileSequence Analysis
Metal bindingi9 – 91Magnesium
Binding sitei10 – 101Phosphate; via amide nitrogen
Metal bindingi11 – 111Magnesium; via carbonyl oxygen
Binding sitei192 – 1921Phosphate
Metal bindingi215 – 2151Magnesium
Metal bindingi216 – 2161Magnesium
Binding sitei218 – 2181PhosphateBy similarity

GO - Molecular functioni

  1. magnesium ion binding Source: UniProtKB
  2. sugar-phosphatase activity Source: EcoCyc

GO - Biological processi

  1. dephosphorylation Source: GOC
  2. small molecule biosynthetic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6425-MONOMER.
ECOL316407:JW0806-MONOMER.
MetaCyc:G6425-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Sugar phosphatase YbiV (EC:3.1.3.23)
Gene namesi
Name:ybiV
Synonyms:supH
Ordered Locus Names:b0822, JW0806
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13327. supH.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: GO_Central
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 271271Sugar phosphatase YbiVPRO_0000054421Add
BLAST

Proteomic databases

PaxDbiP75792.
PRIDEiP75792.

Expressioni

Inductioni

Regulated by the cAMP receptor protein crp.Curated

Gene expression databases

GenevestigatoriP75792.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

IntActiP75792. 10 interactions.
STRINGi511145.b0822.

Structurei

Secondary structure

1
271
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Helixi10 – 145Combined sources
Helixi23 – 3614Combined sources
Beta strandi39 – 435Combined sources
Helixi48 – 514Combined sources
Helixi52 – 543Combined sources
Turni56 – 616Combined sources
Beta strandi62 – 665Combined sources
Helixi67 – 693Combined sources
Beta strandi71 – 744Combined sources
Beta strandi77 – 815Combined sources
Helixi86 – 9712Combined sources
Beta strandi103 – 1108Combined sources
Beta strandi112 – 1154Combined sources
Helixi120 – 1278Combined sources
Beta strandi131 – 1377Combined sources
Helixi139 – 1413Combined sources
Beta strandi146 – 1527Combined sources
Helixi155 – 1573Combined sources
Helixi158 – 16811Combined sources
Turni169 – 1713Combined sources
Beta strandi172 – 1776Combined sources
Beta strandi182 – 1865Combined sources
Helixi192 – 20312Combined sources
Helixi207 – 2093Combined sources
Beta strandi210 – 2145Combined sources
Helixi217 – 2193Combined sources
Helixi220 – 2256Combined sources
Beta strandi227 – 2315Combined sources
Helixi237 – 2426Combined sources
Beta strandi244 – 2463Combined sources
Helixi250 – 2523Combined sources
Helixi254 – 26411Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RLMX-ray1.90A/B/C/D1-271[»]
1RLOX-ray2.00A/B/C/D1-271[»]
1RLTX-ray2.20A/B/C/D1-271[»]
2HF2X-ray1.90A/B1-271[»]
ProteinModelPortaliP75792.
SMRiP75792. Positions 1-270.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP75792.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni44 – 452Phosphate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0561.
HOGENOMiHOG000184782.
InParanoidiP75792.
KOiK07757.
OMAiVKYAFAM.
OrthoDBiEOG6H7FNB.
PhylomeDBiP75792.

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.

P75792-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVKVIVTDM DGTFLNDAKT YNQPRFMAQY QELKKRGIKF VVASGNQYYQ
60 70 80 90 100
LISFFPELKD EISFVAENGA LVYEHGKQLF HGELTRHESR IVIGELLKDK
110 120 130 140 150
QLNFVACGLQ SAYVSENAPE AFVALMAKHY HRLKPVKDYQ EIDDVLFKFS
160 170 180 190 200
LNLPDEQIPL VIDKLHVALD GIMKPVTSGF GFIDLIIPGL HKANGISRLL
210 220 230 240 250
KRWDLSPQNV VAIGDSGNDA EMLKMARYSF AMGNAAENIK QIARYATDDN
260 270
NHEGALNVIQ AVLDNTSPFN S
Length:271
Mass (Da):30,413
Last modified:January 31, 1997 - v1
Checksum:iF8733636B422A9A9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73909.1.
AP009048 Genomic DNA. Translation: BAA35503.1.
PIRiF64819.
RefSeqiNP_415343.1. NC_000913.3.
YP_489095.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73909; AAC73909; b0822.
BAA35503; BAA35503; BAA35503.
GeneIDi12934001.
945432.
KEGGiecj:Y75_p0795.
eco:b0822.
PATRICi32116847. VBIEscCol129921_0849.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73909.1.
AP009048 Genomic DNA. Translation: BAA35503.1.
PIRiF64819.
RefSeqiNP_415343.1. NC_000913.3.
YP_489095.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RLMX-ray1.90A/B/C/D1-271[»]
1RLOX-ray2.00A/B/C/D1-271[»]
1RLTX-ray2.20A/B/C/D1-271[»]
2HF2X-ray1.90A/B1-271[»]
ProteinModelPortaliP75792.
SMRiP75792. Positions 1-270.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP75792. 10 interactions.
STRINGi511145.b0822.

Proteomic databases

PaxDbiP75792.
PRIDEiP75792.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73909; AAC73909; b0822.
BAA35503; BAA35503; BAA35503.
GeneIDi12934001.
945432.
KEGGiecj:Y75_p0795.
eco:b0822.
PATRICi32116847. VBIEscCol129921_0849.

Organism-specific databases

EchoBASEiEB3111.
EcoGeneiEG13327. supH.

Phylogenomic databases

eggNOGiCOG0561.
HOGENOMiHOG000184782.
InParanoidiP75792.
KOiK07757.
OMAiVKYAFAM.
OrthoDBiEOG6H7FNB.
PhylomeDBiP75792.

Enzyme and pathway databases

BioCyciEcoCyc:G6425-MONOMER.
ECOL316407:JW0806-MONOMER.
MetaCyc:G6425-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP75792.
PROiP75792.

Gene expression databases

GenevestigatoriP75792.

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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Enzyme genomics: application of general enzymatic screens to discover new enzymes."
    Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A., Arrowsmith C.H., Edwards A.M., Yakunin A.F.
    FEMS Microbiol. Rev. 29:263-279(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A PHOSPHATASE.
  5. "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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A PHOSPHATASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.
  6. Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PHOSPHATE ANALOGS AND MAGNESIUM ION, FUNCTION AS A PHOSPHATASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT.
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Domain shifting confirms monomeric structure of Escherichia coli sugar phosphatase suph."
    New York structural genomix research consortium (NYSGXRC)
    Submitted (JUN-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-271, SUBUNIT.

Entry informationi

Entry nameiSUPH_ECOLI
AccessioniPrimary (citable) accession number: P75792
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2000
Last sequence update: January 31, 1997
Last modified: February 3, 2015
This is version 121 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.