Sugar phosphatase YidA - Escherichia coli (strain K12)

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P0A8Y5 (YIDA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 69. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Sugar phosphatase YidA
EC=3.1.3.23

Gene names

Name:	yidA
Ordered Locus Names:	b3697, JW3674

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	270 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
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: K_M=0.019 mM for Ery4P (with magnesium ions as cofactor and at pH 9) Ref.6 K_M=0.033 mM for Imido-di-P (with magnesium ions as cofactor and at pH 9) K_M=0.21 mM for Glu1P (with magnesium ions as cofactor and at pH 9) K_M=0.39 mM for Fru1P (with magnesium ions as cofactor and at pH 9) K_M=0.44 mM for Fru6P (with magnesium ions as cofactor and at pH 9) K_M=0.45 mM for Ribu5P (with magnesium ions as cofactor and at pH 9) K_M=0.54 mM for Man1P (with magnesium ions as cofactor and at pH 9) K_M=0.81 mM for Glu6P (with magnesium ions as cofactor and at pH 9) K_M=3.8 mM for Acetyl-P (with magnesium ions as cofactor and at pH 9) pH dependence: Optimum pH is between 6 and 7.5.

Ontologies

Keywords
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Molecular_function	magnesium ion binding Inferred from direct assay Ref.6. Source: EcoliWiki sugar-phosphatase activity Inferred from direct assay Ref.6. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 270

270

Sugar phosphatase YidA

PRO_0000054423

Regions

Region

9 – 11

Substrate By similarity

Sites

Active site

Nucleophile Probable

Metal binding

Magnesium

Metal binding

Magnesium

Metal binding

220

Magnesium

Experimental info

Mutagenesis

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

Secondary structure

270

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A8Y5 [UniParc].

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

270

29,721

        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' referencesShow '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 277:1453-1474(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, 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.

PIR

QQECGB. B65172.

RefSeq

NP_418152.1. NC_000913.2.
YP_491738.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RKQ	X-ray	1.40	A/B	2-270	[»]

ProteinModelPortal

P0A8Y5.

SMR

P0A8Y5. Positions 1-270.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36033N.

IntAct

P0A8Y5. 9 interactions.

MINT

MINT-1238706.

STRING

511145.b3697.

Proteomic databases

PaxDb

P0A8Y5.

PRIDE

P0A8Y5.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76720; AAC76720; b3697.
BAE77597; BAE77597; BAE77597.

GeneID

12933583.
948204.

KEGG

ecj:Y75_p3476.
eco:b3697.

PATRIC

32122889. VBIEscCol129921_3820.

Organism-specific databases

EchoBASE

EB1181.

EcoGene

EG11195. yidA.

Phylogenomic databases

eggNOG

COG0561.

HOGENOM

HOG000184780.

K07024.

OMA

DGHYCIT.

ProtClustDB

PRK10513.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P0A8Y5.

Family and domain databases

Gene3D

3.40.50.1000. 2 hits.

InterPro

IPR023214. HAD-like_dom.
IPR006379. HAD-SF_hydro_IIB.
IPR000150. Hypothet_cof.
[Graphical view]

Pfam

PF00702. Hydrolase. 1 hit.
[Graphical view]

SUPFAM

SSF56784. HAD-like_dom. 1 hit.

TIGRFAMs

TIGR00099. Cof-subfamily. 1 hit.
TIGR01484. HAD-SF-IIB. 1 hit.

PROSITE

PS01228. COF_1. 1 hit.
PS01229. COF_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A8Y5.

Entry information

Entry name

YIDA_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents