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P0A8Y5

- YIDA_ECOLI

UniProt

P0A8Y5 - YIDA_ECOLI

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Protein

Sugar phosphatase YidA

Gene

yidA

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

Functioni

Catalyzes the dephosphorylation of different sugar phosphates including erythrose-4-phosphate (Ery4P), ribose-5-phosphate (Ribu5P), fructose-1-phosphate (Fru1P), fructose-6-phosphate (Fru6P), glucose-6-P (Glu6P), and also imidodiphosphate (Imido-di-P) and acetyl phosphate (Acetyl-P). Selectively hydrolyzes alpha-D-glucose-1-phosphate (Glu1P) and has no activity with the beta form.2 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

  1. KM=0.019 mM for Ery4P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  2. KM=0.033 mM for Imido-di-P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  3. KM=0.21 mM for Glu1P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  4. KM=0.39 mM for Fru1P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  5. KM=0.44 mM for Fru6P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  6. KM=0.45 mM for Ribu5P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  7. KM=0.54 mM for Man1P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  8. KM=0.81 mM for Glu6P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  9. KM=3.8 mM for Acetyl-P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication

pH dependencei

Optimum pH is between 6 and 7.5.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei9 – 91Nucleophile1 Publication
Metal bindingi9 – 91Magnesium
Binding sitei10 – 101Phosphate; via amide nitrogenBy similarity
Metal bindingi11 – 111Magnesium; via carbonyl oxygen
Binding sitei197 – 1971PhosphateBy similarity
Metal bindingi220 – 2201Magnesium
Binding sitei223 – 2231PhosphateBy similarity

GO - Molecular functioni

  1. magnesium ion binding Source: EcoliWiki
  2. phosphatase activity Source: EcoliWiki
  3. sugar-phosphatase activity Source: EcoliWiki

GO - Biological processi

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

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11195-MONOMER.
ECOL316407:JW3674-MONOMER.
MetaCyc:EG11195-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Sugar phosphatase YidA (EC:3.1.3.23)
Gene namesi
Name:yidA
Ordered Locus Names:b3697, JW3674
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11195. yidA.

Subcellular locationi

GO - Cellular componenti

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi9 – 91D → A: Loss of the phosphatase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 270270Sugar phosphatase YidAPRO_0000054423Add
BLAST

Proteomic databases

PaxDbiP0A8Y5.
PRIDEiP0A8Y5.

Expressioni

Gene expression databases

GenevestigatoriP0A8Y5.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

DIPiDIP-36033N.
IntActiP0A8Y5. 10 interactions.
MINTiMINT-1238706.
STRINGi511145.b3697.

Structurei

Secondary structure

1
270
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Helixi10 – 145Combined sources
Helixi23 – 3412Combined sources
Beta strandi38 – 425Combined sources
Helixi47 – 493Combined sources
Helixi51 – 566Combined sources
Beta strandi65 – 684Combined sources
Helixi69 – 713Combined sources
Beta strandi73 – 764Combined sources
Turni77 – 793Combined sources
Beta strandi82 – 854Combined sources
Helixi90 – 10314Combined sources
Beta strandi106 – 1105Combined sources
Beta strandi115 – 1173Combined sources
Helixi124 – 1329Combined sources
Beta strandi137 – 1393Combined sources
Helixi142 – 1443Combined sources
Beta strandi153 – 1575Combined sources
Helixi160 – 16910Combined sources
Helixi172 – 1776Combined sources
Beta strandi178 – 1847Combined sources
Beta strandi187 – 1926Combined sources
Helixi197 – 20812Combined sources
Helixi212 – 2143Combined sources
Beta strandi215 – 2195Combined sources
Helixi222 – 2243Combined sources
Helixi225 – 2306Combined sources
Beta strandi231 – 2366Combined sources
Helixi242 – 2476Combined sources
Beta strandi249 – 2513Combined sources
Turni255 – 2584Combined sources
Helixi259 – 2679Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RKQX-ray1.40A/B2-270[»]
ProteinModelPortaliP0A8Y5.
SMRiP0A8Y5. Positions 1-270.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8Y5.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni43 – 442Phosphate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0561.
HOGENOMiHOG000184780.
InParanoidiP0A8Y5.
KOiK07024.
OMAiLGVHFHA.
OrthoDBiEOG6K13W0.
PhylomeDBiP0A8Y5.

Family and domain databases

Gene3Di3.40.50.1000. 2 hits.
InterProiIPR023214. HAD-like_dom.
IPR006379. HAD-SF_hydro_IIB.
IPR000150. Hypothet_cof.
[Graphical view]
PfamiPF00702. Hydrolase. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR00099. Cof-subfamily. 1 hit.
TIGR01484. HAD-SF-IIB. 1 hit.
PROSITEiPS01228. COF_1. 1 hit.
PS01229. COF_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A8Y5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAIKLIAIDM DGTLLLPDHT ISPAVKNAIA AARARGVNVV LTTGRPYAGV
60 70 80 90 100
HNYLKELHME QPGDYCITYN GALVQKAADG STVAQTALSY DDYRFLEKLS
110 120 130 140 150
REVGSHFHAL DRTTLYTANR DISYYTVHES FVATIPLVFC EAEKMDPNTQ
160 170 180 190 200
FLKVMMIDEP AILDQAIARI PQEVKEKYTV LKSAPYFLEI LDKRVNKGTG
210 220 230 240 250
VKSLADVLGI KPEEIMAIGD QENDIAMIEY AGVGVAMDNA IPSVKEVANF
260 270
VTKSNLEDGV AFAIEKYVLN
Length:270
Mass (Da):29,721
Last modified:June 21, 2005 - v1
Checksum:i04E749788D8A9446
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10328 Genomic DNA. Translation: AAA62048.1.
U00096 Genomic DNA. Translation: AAC76720.1.
AP009048 Genomic DNA. Translation: BAE77597.1.
X04341 Genomic DNA. Translation: CAA27873.1.
PIRiB65172. QQECGB.
RefSeqiNP_418152.1. NC_000913.3.
YP_491738.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76720; AAC76720; b3697.
BAE77597; BAE77597; BAE77597.
GeneIDi12933583.
948204.
KEGGiecj:Y75_p3476.
eco:b3697.
PATRICi32122889. VBIEscCol129921_3820.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10328 Genomic DNA. Translation: AAA62048.1 .
U00096 Genomic DNA. Translation: AAC76720.1 .
AP009048 Genomic DNA. Translation: BAE77597.1 .
X04341 Genomic DNA. Translation: CAA27873.1 .
PIRi B65172. QQECGB.
RefSeqi NP_418152.1. NC_000913.3.
YP_491738.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1RKQ X-ray 1.40 A/B 2-270 [» ]
ProteinModelPortali P0A8Y5.
SMRi P0A8Y5. Positions 1-270.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36033N.
IntActi P0A8Y5. 10 interactions.
MINTi MINT-1238706.
STRINGi 511145.b3697.

Proteomic databases

PaxDbi P0A8Y5.
PRIDEi P0A8Y5.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76720 ; AAC76720 ; b3697 .
BAE77597 ; BAE77597 ; BAE77597 .
GeneIDi 12933583.
948204.
KEGGi ecj:Y75_p3476.
eco:b3697.
PATRICi 32122889. VBIEscCol129921_3820.

Organism-specific databases

EchoBASEi EB1181.
EcoGenei EG11195. yidA.

Phylogenomic databases

eggNOGi COG0561.
HOGENOMi HOG000184780.
InParanoidi P0A8Y5.
KOi K07024.
OMAi LGVHFHA.
OrthoDBi EOG6K13W0.
PhylomeDBi P0A8Y5.

Enzyme and pathway databases

BioCyci EcoCyc:EG11195-MONOMER.
ECOL316407:JW3674-MONOMER.
MetaCyc:EG11195-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0A8Y5.
PROi P0A8Y5.

Gene expression databases

Genevestigatori P0A8Y5.

Family and domain databases

Gene3Di 3.40.50.1000. 2 hits.
InterProi IPR023214. HAD-like_dom.
IPR006379. HAD-SF_hydro_IIB.
IPR000150. Hypothet_cof.
[Graphical view ]
Pfami PF00702. Hydrolase. 1 hit.
[Graphical view ]
SUPFAMi SSF56784. SSF56784. 1 hit.
TIGRFAMsi TIGR00099. Cof-subfamily. 1 hit.
TIGR01484. HAD-SF-IIB. 1 hit.
PROSITEi PS01228. COF_1. 1 hit.
PS01229. COF_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
    Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
    Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  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(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy."
    Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H., Gellert M., Mizuuchi K.
    Nucleic Acids Res. 15:771-784(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-195.
  5. "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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A PHOSPHATASE.
  6. "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, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF ASP-9, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.
  7. "Crystal structure of NYSGRC target T1436: a hypothetical protein YidA."
    Ramagopal U.A., Almo S.C.
    Submitted (MAR-2004) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 2-270 IN COMPLEX WITH MAGNESIUM IONS, SUBUNIT.

Entry informationi

Entry nameiYIDA_ECOLI
AccessioniPrimary (citable) accession number: P0A8Y5
Secondary accession number(s): P09997, P76737, Q2M809
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 21, 2005
Last sequence update: June 21, 2005
Last modified: November 26, 2014
This is version 82 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