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P0A8Y5 (YIDA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 76. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Sugar phosphatase YidA

EC=3.1.3.23
Gene names
Name:yidA
Ordered Locus Names:b3697, JW3674
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length270 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.6

Catalytic activity

Sugar phosphate + H2O = sugar + phosphate. Ref.6

Cofactor

Magnesium. Can also use other divalent metal cations as manganese, cobalt and zinc. Ref.6

Subunit structure

Homodimer. Ref.7

Sequence similarities

Belongs to the HAD-like hydrolase superfamily. Cof family.

Biophysicochemical properties

Kinetic parameters:

KM=0.019 mM for Ery4P (in the presence of magnesium ion as cofactor and at pH 9) Ref.6

KM=0.033 mM for Imido-di-P (in the presence of magnesium ion as cofactor and at pH 9)

KM=0.21 mM for Glu1P (in the presence of magnesium ion as cofactor and at pH 9)

KM=0.39 mM for Fru1P (in the presence of magnesium ion as cofactor and at pH 9)

KM=0.44 mM for Fru6P (in the presence of magnesium ion as cofactor and at pH 9)

KM=0.45 mM for Ribu5P (in the presence of magnesium ion as cofactor and at pH 9)

KM=0.54 mM for Man1P (in the presence of magnesium ion as cofactor and at pH 9)

KM=0.81 mM for Glu6P (in the presence of magnesium ion as cofactor and at pH 9)

KM=3.8 mM for Acetyl-P (in the presence of magnesium ion as cofactor and at pH 9)

pH dependence:

Optimum pH is between 6 and 7.5.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 270270Sugar phosphatase YidA
PRO_0000054423

Regions

Region43 – 442Phosphate binding By similarity

Sites

Active site91Nucleophile Ref.6
Metal binding91Magnesium
Metal binding111Magnesium; via carbonyl oxygen
Metal binding2201Magnesium
Binding site101Phosphate; via amide nitrogen By similarity
Binding site1971Phosphate By similarity
Binding site2231Phosphate By similarity

Experimental info

Mutagenesis91D → A: Loss of the phosphatase activity. Ref.6

Secondary structure

.......................................................... 270
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A8Y5 [UniParc].

Last modified June 21, 2005. Version 1.
Checksum: 04E749788D8A9446

FASTA27029,721
        10         20         30         40         50         60 
MAIKLIAIDM DGTLLLPDHT ISPAVKNAIA AARARGVNVV LTTGRPYAGV HNYLKELHME 

        70         80         90        100        110        120 
QPGDYCITYN GALVQKAADG STVAQTALSY DDYRFLEKLS REVGSHFHAL DRTTLYTANR 

       130        140        150        160        170        180 
DISYYTVHES FVATIPLVFC EAEKMDPNTQ FLKVMMIDEP AILDQAIARI PQEVKEKYTV 

       190        200        210        220        230        240 
LKSAPYFLEI LDKRVNKGTG VKSLADVLGI KPEEIMAIGD QENDIAMIEY AGVGVAMDNA 

       250        260        270 
IPSVKEVANF VTKSNLEDGV AFAIEKYVLN 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L10328 Genomic DNA. Translation: AAA62048.1.
U00096 Genomic DNA. Translation: AAC76720.1.
AP009048 Genomic DNA. Translation: BAE77597.1.
X04341 Genomic DNA. Translation: CAA27873.1.
PIRQQECGB. B65172.
RefSeqNP_418152.1. NC_000913.3.
YP_491738.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1RKQX-ray1.40A/B2-270[»]
ProteinModelPortalP0A8Y5.
SMRP0A8Y5. Positions 1-270.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36033N.
IntActP0A8Y5. 10 interactions.
MINTMINT-1238706.
STRING511145.b3697.

Proteomic databases

PaxDbP0A8Y5.
PRIDEP0A8Y5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76720; AAC76720; b3697.
BAE77597; BAE77597; BAE77597.
GeneID12933583.
948204.
KEGGecj:Y75_p3476.
eco:b3697.
PATRIC32122889. VBIEscCol129921_3820.

Organism-specific databases

EchoBASEEB1181.
EcoGeneEG11195. yidA.

Phylogenomic databases

eggNOGCOG0561.
HOGENOMHOG000184780.
KOK07024.
OMARYTIMKS.
OrthoDBEOG6K13W0.
PhylomeDBP0A8Y5.
ProtClustDBPRK10513.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0A8Y5.

Family and domain databases

Gene3D3.40.50.1000. 2 hits.
InterProIPR023214. HAD-like_dom.
IPR006379. HAD-SF_hydro_IIB.
IPR000150. Hypothet_cof.
[Graphical view]
PfamPF00702. Hydrolase. 1 hit.
[Graphical view]
SUPFAMSSF56784. SSF56784. 1 hit.
TIGRFAMsTIGR00099. Cof-subfamily. 1 hit.
TIGR01484. HAD-SF-IIB. 1 hit.
PROSITEPS01228. COF_1. 1 hit.
PS01229. COF_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0A8Y5.
PROP0A8Y5.

Entry information

Entry nameYIDA_ECOLI
AccessionPrimary (citable) accession number: P0A8Y5
Secondary accession number(s): P09997, P76737, Q2M809
Entry history
Integrated into UniProtKB/Swiss-Prot: June 21, 2005
Last sequence update: June 21, 2005
Last modified: April 16, 2014
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene