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Escherichia coli K-12 substr. MG1655 Enzyme: glycerophosphodiester phosphodiesterase, cytosolic



Gene: ugpQ Accession Numbers: EG11050 (EcoCyc), b3449, ECK3433

Regulation Summary Diagram: ?

Summary:
UgpQ is a cytosolic glycerophosphodiester phosphodiesterase with broad substrate specificity [Ohshima08].

Initial experiments suggested that cytoplasmic glycerophosphodiesters are not substrates of UgpQ, and that they are hydrolyzed only when transported by the Ugp system [Brzoska88]. However, recent purification and characterization of the enzyme contradicts those results [Ohshima08]. Moreover, purified UgpQ does not affect the activity of the UgpB-EAC2 transporter complex in vitro [Wuttge12].

Expression of UgpQ is induced by phosphate starvation [Ohshima08]. The ugp operon is induced by carbon starvation during the late logarithmic growth phase [Su91a].

UgpQ: "uptake of glycerol phosphate" [Argast78]

Citations: [Tommassen91]

Gene Citations: [Overduin88]

Locations: cytosol

Map Position: [3,585,393 <- 3,586,136] (77.28 centisomes)
Length: 744 bp / 247 aa

Molecular Weight of Polypeptide: 27.41 kD (from nucleotide sequence), 27.0 kD (experimental) [Ohshima08 ]

pI: 6.48

Isozyme Sequence Similarity:
GlpQ: NO

Unification Links: ASAP:ABE-0011264 , CGSC:33697 , EchoBASE:EB1043 , EcoGene:EG11050 , EcoliWiki:b3449 , ModBase:P10908 , OU-Microarray:b3449 , PortEco:ugpQ , Pride:P10908 , Protein Model Portal:P10908 , RefSeq:NP_417906 , RegulonDB:EG11050 , SMR:P10908 , String:511145.b3449 , Swiss-Model:P10908 , UniProt:P10908

Relationship Links: InterPro:IN-FAMILY:IPR004129 , InterPro:IN-FAMILY:IPR017946 , Panther:IN-FAMILY:PTHR23344 , Pfam:IN-FAMILY:PF03009

Gene-Reaction Schematic: ?

Instance reaction of [a glycerophosphodiester + H2O → an alcohol + sn-glycerol 3-phosphate + H+] (3.1.4.46):
i1: glycerophosphoglycerol + H2O → glycerol + sn-glycerol 3-phosphate + H+ (3.1.4.46)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006071 - glycerol metabolic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006629 - lipid metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Ohshima08]
GO:0008889 - glycerophosphodiester phosphodiesterase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Ohshima08]
GO:0047389 - glycerophosphocholine phosphodiesterase activity Inferred from experiment [Ohshima08]
GO:0047395 - glycerophosphoinositol glycerophosphodiesterase activity Inferred from experiment [Ohshima08]
GO:0008081 - phosphoric diester hydrolase activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism misc. glycerol metabolism

Essentiality data for ugpQ 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 14-Oct-2013 by Keseler I , SRI International


Enzymatic reaction of: glycerophosphodiester phosphodiesterase

Synonyms: glycerophosphoryl diester phosphodiesterase, glycerophosphodiester glycerophosphohydrolase

EC Number: 3.1.4.46

a glycerophosphodiester + H2O <=> an alcohol + sn-glycerol 3-phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

Alternative Substrates for a glycerophosphodiester: a glycerophosphoinositol [Ohshima08 ] , sn-glycero-3-phosphocholine [Ohshima08 ]

In Pathways: glycerol and glycerophosphodiester degradation , glycerophosphodiester degradation

Summary:
Mn2+ and Co2+ can also serve as the divalent cation cofactor [Ohshima08].

Cofactors or Prosthetic Groups: Mg2+ [Ohshima08]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
a glycerophosphoinositol
390.0
1.8
[Ohshima08]
sn-glycero-3-phosphocholine
2000.0
3.2
[Ohshima08]

pH(opt): 7.5 [Ohshima08]


Enzymatic reaction of: glycerophosphoglycerol phosphodiesterase (glycerophosphodiester phosphodiesterase, cytosolic)

EC Number: 3.1.4.46

glycerophosphoglycerol + H2O <=> glycerol + sn-glycerol 3-phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Ohshima08]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
glycerophosphoglycerol
620.0
3.3
[Ohshima08]


Enzymatic reaction of: glycerophosphoserine phosphodiesterase (glycerophosphodiester phosphodiesterase, cytosolic)

EC Number: 3.1.4.46

glycerophosphoserine + H2O <=> sn-glycerol 3-phosphate + L-serine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Ohshima08]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
glycerophosphoserine
660.0
2.8
[Ohshima08]


Enzymatic reaction of: L-1-glycerophophorylethanolamine phosphodiesterase (glycerophosphodiester phosphodiesterase, cytosolic)

EC Number: 3.1.4.46

sn-glycero-3-phosphoethanolamine + H2O <=> sn-glycerol 3-phosphate + ethanolamine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Ohshima08]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
sn-glycero-3-phosphoethanolamine
220.0
1.1
[Ohshima08]


Sequence Features

Feature Class Location Citations
Cleavage-of-Initial-Methionine 1
[Ohshima08]


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3449 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11050; confirmed by SwissProt match.


References

Argast78: Argast M, Ludtke D, Silhavy TJ, Boos W (1978). "A second transport system for sn-glycerol-3-phosphate in Escherichia coli." J Bacteriol 136(3);1070-83. PMID: 363686

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

Brzoska88: Brzoska P, Boos W (1988). "Characteristics of a ugp-encoded and phoB-dependent glycerophosphoryl diester phosphodiesterase which is physically dependent on the ugp transport system of Escherichia coli." J Bacteriol 1988;170(9);4125-35. PMID: 2842304

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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.

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

Ohshima08: Ohshima N, Yamashita S, Takahashi N, Kuroishi C, Shiro Y, Takio K (2008). "Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (UgpQ) requires Mg2+, Co2+, or Mn2+ for its enzyme activity." J Bacteriol 190(4);1219-23. PMID: 18083802

Overduin88: Overduin P, Boos W, Tommassen J (1988). "Nucleotide sequence of the ugp genes of Escherichia coli K-12: homology to the maltose system." Mol Microbiol 2(6);767-75. PMID: 3062310

Su91a: Su TZ, Schweizer HP, Oxender DL (1991). "Carbon-starvation induction of the ugp operon, encoding the binding protein-dependent sn-glycerol-3-phosphate transport system in Escherichia coli." Mol Gen Genet 230(1-2);28-32. PMID: 1745236

Tommassen91: Tommassen J, Eiglmeier K, Cole ST, Overduin P, Larson TJ, Boos W (1991). "Characterization of two genes, glpQ and ugpQ, encoding glycerophosphoryl diester phosphodiesterases of Escherichia coli." Mol Gen Genet 1991;226(1-2);321-7. PMID: 1851953

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Wuttge12: Wuttge S, Bommer M, Jager F, Martins BM, Jacob S, Licht A, Scheffel F, Dobbek H, Schneider E (2012). "Determinants of substrate specificity and biochemical properties of the sn-glycerol-3-phosphate ATP binding cassette transporter (UgpB-AEC2 ) of Escherichia coli." Mol Microbiol 86(4);908-20. PMID: 23013274

Other References Related to Gene Regulation

Kasahara91: Kasahara M, Makino K, Amemura M, Nakata A, Shinagawa H (1991). "Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters." J Bacteriol 1991;173(2);549-58. PMID: 1987150

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360


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 18.5 on Sun Dec 21, 2014, biocyc14.