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Escherichia coli K-12 substr. MG1655 Enzyme: sugar phosphatase



Gene: yidA Accession Numbers: EG11195 (EcoCyc), b3697, ECK3689

Regulation Summary Diagram: ?

Regulation summary diagram for yidA

Summary:
YidA is a promiscuous sugar phosphatase belonging to the superfamily of haloacid dehalogenase (HAD)-like hydrolases. Its preferred substrate is erythrose-4-phosphate [Kuznetsova06]. YidA selectively hydrolyzes α-D-glucose-1-phosphate and has no activity with the β form [Kuznetsova06, Wildberger14]. The reaction proceeds via the canonical phosphomonoester hydrolase mechanism, which involves breakage of the P-O bond, not the C1-O bond [Wildberger14]. The phosphatase activity of YidA was first discovered in a high-throughput screen of purified proteins [Kuznetsova05].

Mutagenesis of the predicted catalytic Asp residue in YidA results in loss of phosphatase activity [Kuznetsova06]. YidA does not catalyze phosphoryl transfer to a sugar acceptor [Wildberger14].

Locations: cytosol

Map Position: [3,874,163 <- 3,874,975] (83.5 centisomes, 301°)
Length: 813 bp / 270 aa

Molecular Weight of Polypeptide: 29.721 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012086 , DIP:DIP-36033N , EchoBASE:EB1181 , EcoGene:EG11195 , EcoliWiki:b3697 , Mint:MINT-1238706 , ModBase:P0A8Y5 , OU-Microarray:b3697 , PortEco:yidA , Pride:P0A8Y5 , Protein Model Portal:P0A8Y5 , RefSeq:NP_418152 , RegulonDB:EG11195 , SMR:P0A8Y5 , String:511145.b3697 , Swiss-Model:P0A8Y5 , UniProt:P0A8Y5

Relationship Links: InterPro:IN-FAMILY:IPR000150 , InterPro:IN-FAMILY:IPR006379 , InterPro:IN-FAMILY:IPR023214 , PDB:Structure:1RKQ , Pfam:IN-FAMILY:PF00702 , Prosite:IN-FAMILY:PS01228 , Prosite:IN-FAMILY:PS01229

In Paralogous Gene Group: 129 (5 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Instance reaction of [D-glucopyranose 6-phosphate[periplasmic space] + H2O[periplasmic space] → D-glucopyranose[periplasmic space] + phosphate[periplasmic space]] (3.1.3.9/3.1.3.58):
i1: α-D-glucose 6-phosphate + H2O → α-D-glucose + phosphate (3.1.3.9/3.1.3.58)

Instance reactions of [a sugar phosphate + H2O → a sugar + phosphate] (3.1.3.23):
i2: β-D-glucose 6-phosphate + H2O → β-D-glucose + phosphate (3.1.3.9/3.1.3.58)

i3: D-glucopyranose 6-phosphate[periplasmic space] + H2O[periplasmic space] → D-glucopyranose[periplasmic space] + phosphate[periplasmic space] (3.1.3.9/3.1.3.58)

i4: α-D-glucose 1-phosphate + H2O → D-glucopyranose + phosphate (3.1.3.10)

i5: D-ribose 5-phosphate[periplasmic space] + H2O[periplasmic space]aldehydo-D-ribose[periplasmic space] + phosphate[periplasmic space] (3.1.3.-)

i6: a hexose phosphate + H2O = a hexose + phosphate (3.1.3.-)

i7: β-D-fructofuranose 1-phosphate + H2O → β-D-fructofuranose + phosphate (3.1.3.-)

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01a, Kuznetsova06]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0044283 - small molecule biosynthetic process Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Kuznetsova06]
GO:0016791 - phosphatase activity Inferred from experiment [Kuznetsova06]
GO:0050308 - sugar-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, Wildberger14, Kuznetsova06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]

Gene Class: UNCLASSIFIED

Essentiality data for yidA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Curated 17-Mar-2010 by Fulcher C , SRI International
Last-Curated ? 23-Dec-2014 by Keseler I , SRI International


Enzymatic reaction of: sugar phosphatase

Synonyms: HAD13

EC Number: 3.1.3.23

a sugar phosphate + H2O <=> a sugar + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a sugar phosphate: D-fructose 1-phosphate [Kuznetsova06 ] , D-erythrose 4-phosphate [Kuznetsova06 ] , α-D-mannose 1-phosphate [Kuznetsova06 ] , α-D-glucose 1-phosphate [Wildberger14 , Kuznetsova06 ] , D-ribose 5-phosphate [Kuznetsova06 ] , imidodiphosphate [Kuznetsova06 ]

In Pathways: glucose and glucose-1-phosphate degradation

Summary:
Kms for the various sugar phosphate substrates range between 19 and 810 µM [Kuznetsova06].

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
imidodiphosphate
33.0
14.0
0.42
[Kuznetsova06]
D-fructose 1-phosphate
390.0
11.0
0.028
[Kuznetsova06]
α-D-glucose 1-phosphate
210.0
20.0
0.095
[Kuznetsova06]
α-D-glucose 1-phosphate
12.0
[Wildberger14]
D-erythrose 4-phosphate
19.0
19.0
1.0
[Kuznetsova06]
α-D-mannose 1-phosphate
530.0
21.0
0.04
[Kuznetsova06]
D-ribose 5-phosphate
450.0
9.2
0.02
[Kuznetsova06]


Sequence Features

Protein sequence of sugar phosphatase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 9
[UniProt15]
UniProt: Magnesium.
Active-Site 9
[Kuznetsova06, UniProt15]
UniProt: Nucleophile.
Mutagenesis-Variant 9
[Kuznetsova06, UniProt12b]
UniProt: Loss of the phosphatase activity.
Amino-Acid-Sites-That-Bind 10
[UniProt15]
UniProt: Phosphate; via amide nitrogen.
Metal-Binding-Site 11
[UniProt15]
UniProt: Magnesium; via carbonyl oxygen.
Protein-Segment 43 -> 44
[UniProt14a]
UniProt: Phosphate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 197
[UniProt15]
UniProt: Phosphate.
Metal-Binding-Site 220
[UniProt15]
UniProt: Magnesium.
Amino-Acid-Sites-That-Bind 223
[UniProt15]
UniProt: Phosphate.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b3697 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11195; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kuznetsova05: Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF (2005). "Enzyme genomics: Application of general enzymatic screens to discover new enzymes." FEMS Microbiol Rev 29(2);263-79. PMID: 15808744

Kuznetsova06: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF (2006). "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." J Biol Chem 281(47):36149-61. PMID: 16990279

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-14 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wildberger14: Wildberger P, Pfeiffer M, Brecker L, Rechberger GN, Birner-Gruenberger R, Nidetzky B (2014). "Phosphoryl transfer from α-d-glucose 1-phosphate catalyzed by Escherichia coli sugar-phosphate phosphatases of two protein-superfamily types." Appl Environ Microbiol. PMID: 25527541


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed May 27, 2015, BIOCYC14A.