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Escherichia coli K-12 substr. MG1655 Enzyme: glycerophosphoryl diester phosphodiesterase, periplasmic



Gene: glpQ Accession Numbers: EG10399 (EcoCyc), b2239, ECK2231

Regulation Summary Diagram: ?

Subunit composition of glycerophosphoryl diester phosphodiesterase, periplasmic = [GlpQ]2

Summary:
Glycerophosphoryl diester phosphodiesterase (GlpQ) is involved in the utilization of the glycerol moiety of phospholipids and triglycerides after their breakdown into usable forms such as glycerophosphodiesters, sn-glycerol-3-phosphate (G3P) or glycerol. GlpQ catalyzes the hydrolysis of glycerophosphodiesters into sn-glycerol 3-phosphate (glycerol-P) and an alcohol. The glycerol-P is then transported into the cell by the glycerol-P transporter, GlpT [Larson83, Larson88]

Periplasmic GlpQ is specific for the glycerophospho- moiety of the substrate, but the alcohol can be any one of several alcohols. This provides the cell with the capability of channeling a wide variety of glycerophosphodiesters into the glp-encoded dissimilatory system [Larson83, Silhavy76]

glpQ is part of the glpTQ operon where glpT encodes the glycerol-P transporter [Larson83]. Regulatory elements of the glpTQ operon have been identified [Yang97].

Comparison of the nucleotide sequences of glpQ with ugpQ, which codes for another phosphodiesterase, showed significant similarity in primary structure. glpQ encodes a periplasmic protein with a signal sequence. [Tommassen91]

Citations: [HenggeAronis86]

Gene Citations: [Larson92]

Locations: periplasmic space

Map Position: [2,347,957 <- 2,349,033] (50.61 centisomes)
Length: 1077 bp / 358 aa

Molecular Weight of Polypeptide: 40.843 kD (from nucleotide sequence), 40.0 kD (experimental) [Larson88 ]

Molecular Weight of Multimer: 70.0 kD (experimental) [Larson88]

pI: 5.66

Isozyme Sequence Similarity:
glycerophosphodiester phosphodiesterase, cytosolic: NO

Unification Links: ASAP:ABE-0007399 , CGSC:690 , EchoBASE:EB0394 , EcoGene:EG10399 , EcoliWiki:b2239 , ModBase:P09394 , OU-Microarray:b2239 , PortEco:glpQ , Pride:P09394 , Protein Model Portal:P09394 , RefSeq:NP_416742 , RegulonDB:EG10399 , SMR:P09394 , String:511145.b2239 , UniProt:P09394

Relationship Links: InterPro:IN-FAMILY:IPR004129 , InterPro:IN-FAMILY:IPR017946 , Panther:IN-FAMILY:PTHR23344 , PDB:Structure:1T8Q , PDB:Structure:1YDY , 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:0005509 - calcium ion binding Inferred from experiment [Larson88]
GO:0008889 - glycerophosphodiester phosphodiesterase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Larson88]
GO:0042802 - identical protein binding Inferred from experiment [Larson88]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Larson88]
GO:0008081 - phosphoric diester hydrolase activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0042597 - periplasmic space Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Silhavy76]

MultiFun Terms: metabolism central intermediary metabolism misc. glycerol metabolism

Essentiality data for glpQ 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 ? 22-Oct-2013 by Kubo A , SRI International


Enzymatic reaction of: glycerophosphoryl diester phosphodiesterase, periplasmic

Synonyms: GDP, glycerophosphodiester 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 [Comment 5 ]: a glycerophosphoinositol [Larson88 ] , glycerophosphoserine [Larson88 ] , bis(glycerophosphoglycerol) [Larson88 ] , glycerophosphoglycerol [Larson88 ] , an L-1-phosphatidyl-ethanolamine [Larson88 ] , sn-glycero-3-phosphocholine [Larson88 ]

In Pathways: glycerol and glycerophosphodiester degradation , glycerophosphodiester degradation

Cofactors or Prosthetic Groups: Ca2+ [Larson88, Larson83]

Kinetic Parameters:

Substrate
Km (μM)
Citations
glycerophosphoglycerol
350.0
[Larson88]
an L-1-phosphatidyl-ethanolamine
240.0
[Larson88]
a glycerophosphoinositol
1000.0
[Larson88]
sn-glycero-3-phosphocholine
280.0
[Larson88]
glycerophosphoserine
590.0
[Larson88]

pH(opt) (forward direction): 7.8 [Larson88]

pH(opt): 7.5 [BRENDA14, Ohshima08], 9 [BRENDA14, Larson83]


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 25
[GonzalezGil96, Tommassen91, UniProt11]
.
Chain 26 -> 358
[UniProt09]
UniProt: Glycerophosphoryl diester phosphodiesterase;
Sequence-Conflict 27
[GonzalezGil96, UniProt10a]
Alternate sequence: D → I; UniProt: (in Ref. 6; AA sequence);
Metal-Binding-Site 63
[UniProt10a]
UniProt: Calcium;
Metal-Binding-Site 65
[UniProt10a]
UniProt: Calcium;
Metal-Binding-Site 171
[UniProt10a]
UniProt: Calcium;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2239 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10399; 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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.

GonzalezGil96: Gonzalez-Gil G, Bringmann P, Kahmann R (1996). "FIS is a regulator of metabolism in Escherichia coli." Mol Microbiol 22(1);21-9. PMID: 8899705

HenggeAronis86: Hengge-Aronis R, Boos W (1986). "Translational control of exported proteins in Escherichia coli." J Bacteriol 167(2);462-6. PMID: 3015871

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

Larson83: Larson TJ, Ehrmann M, Boos W (1983). "Periplasmic glycerophosphodiester phosphodiesterase of Escherichia coli, a new enzyme of the glp regulon." J Biol Chem 1983;258(9);5428-32. PMID: 6304089

Larson88: Larson TJ, van Loo-Bhattacharya AT (1988). "Purification and characterization of glpQ-encoded glycerophosphodiester phosphodiesterase from Escherichia coli K-12." Arch Biochem Biophys 1988;260(2);577-84. PMID: 2829735

Larson92: Larson TJ, Cantwell JS, van Loo-Bhattacharya AT (1992). "Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12." J Biol Chem 1992;267(9);6114-21. PMID: 1556120

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

Silhavy76: Silhavy TJ, Hartig-Beecken I, Boos W (1976). "Periplasmic protein related to the sn-glycerol-3-phosphate transport system of Escherichia coli." J Bacteriol 126(2);951-8. PMID: 770459

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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."

Yang97: Yang B, Gerhardt SG, Larson TJ (1997). "Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12." Mol Microbiol 24(3);511-21. PMID: 9179845

Other References Related to Gene Regulation

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Kuritzkes84: Kuritzkes DR, Zhang XY, Lin EC (1984). "Use of phi(glp-lac) in studies of respiratory regulation of the Escherichia coli anaerobic sn-glycerol-3-phosphate dehydrogenase genes (glpAB)." J Bacteriol 157(2);591-8. PMID: 6363389

Weissenborn92: Weissenborn DL, Wittekindt N, Larson TJ (1992). "Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12." J Biol Chem 1992;267(9);6122-31. PMID: 1372899

Wong92: Wong KK, Kwan HS (1992). "Transcription of glpT of Escherichia coli K12 is regulated by anaerobiosis and fnr." FEMS Microbiol Lett 1992;73(1-2);15-8. PMID: 1521763

Zhao94a: Zhao N, Oh W, Trybul D, Thrasher KS, Kingsbury TJ, Larson TJ (1994). "Characterization of the interaction of the glp repressor of Escherichia coli K-12 with single and tandem glp operator variants." J Bacteriol 176(8);2393-7. PMID: 8157609

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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 Wed Nov 26, 2014, biocyc13.