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Escherichia coli K-12 substr. MG1655 Enzyme: glycogen synthase



Gene: glgA Accession Numbers: EG10377 (EcoCyc), b3429, ECK3415

Regulation Summary Diagram: ?

Summary:
Glycogen synthase is a glycosyltransferase, the second enzyme in the glycogen biosynthesis pathway. It catalyzes the addition of a glucosyl unit from ADP-glucose to the non-reducing end of glycogen.

Lys15 may be involved in binding of ADP-glucose [Furukawa90, Furukawa93a]. A conserved region around Cys379 is predicted to form a loop structure and is involved in the interaction with ADP-glucose [Yep04]. Lys277 may be required for catalysis [Furukawa94]. Further site-directed mutagenesis identified residues essential for catalytic activity [Yep04a] and ADP-glucose binding [Yep06].

Crystal structures of the wild-type and mutant GlgA in various conformations have been solved, suggesting the location of catalytic residues [Sheng09]. A structure of GlgA with bound oligosaccharide indicates that long-chain glycans only bind to the N-terminal domain, ensuring unencumbered interdomain movement and efficient catalysis [Sheng09a].

Native glycogen synthase binds to metal affinity columns and may thus bind Mg2+, like its human homolog [BolanosGarcia06].

Glycogen synthase from E. coli B can exist in homodimeric, -trimeric and -tetrameric form [Fox76]. However, all crystal structures obtained of the K-12 enzyme show a monomeric form [Sheng09].

Review: [Cid02]
In a gene expression analysis, RpoS positively regulated glgA gene in the stationary phase. Its effect could be indirect [BeckerHapak95].

Gene Citations: [Montero10, Romeo88, Romeo89, Yang96]

Locations: cytosol

Map Position: [3,564,623 <- 3,566,056] (76.83 centisomes)
Length: 1434 bp / 477 aa

Molecular Weight of Polypeptide: 52.822 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011200 , CGSC:710 , EchoBASE:EB0372 , EcoGene:EG10377 , EcoliWiki:B3429 , ModBase:P0A6U8 , OU-Microarray:b3429 , PortEco:glgA , PR:PRO_000022776 , Pride:P0A6U8 , Protein Model Portal:P0A6U8 , RefSeq:NP_417887 , RegulonDB:EG10377 , SMR:P0A6U8 , String:511145.b3429 , Swiss-Model:P0A6U8 , UniProt:P0A6U8

Relationship Links: InterPro:IN-FAMILY:IPR001296 , InterPro:IN-FAMILY:IPR011835 , InterPro:IN-FAMILY:IPR013534 , PDB:Structure:2QZS , PDB:Structure:2R4T , PDB:Structure:2R4U , PDB:Structure:3COP , PDB:Structure:3CX4 , PDB:Structure:3D1J , PDB:Structure:3GUH , Pfam:IN-FAMILY:PF00534 , Pfam:IN-FAMILY:PF08323

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0005978 - glycogen biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, MoranZorzano07]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01a]
GO:0009250 - glucan biosynthetic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0009011 - starch synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Furukawa93a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016757 - transferase activity, transferring glycosyl groups Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) cytoplasmic polysaccharides

Essentiality data for glgA 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 ? 13-Nov-2009 by Keseler I , SRI International


Enzymatic reaction of: glycogen synthase

Synonyms: ADP-glucose-starch glucosyltransferase, ADPglucose:1,4-α-D-glucan 4-α-D-glucosyltransferase

EC Number: 2.4.1.21

(1,4-α-D-glucosyl)(n) + ADP-α-D-glucose <=> ADP + (1,4-α-D-glucosyl)(n+1)

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

This reaction is reversible.

In Pathways: glycogen biosynthesis I (from ADP-D-Glucose)

Summary:
The Ki for ADP is 30 µM at pH 8.5 [Furukawa93a].

Inhibitors (Competitive): ADP [Furukawa93a, Comment 5]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ADP-α-D-glucose
35.0
[Fox76, BRENDA, 2014]
ADP-α-D-glucose
11.0
[Yep06]

pH(opt): 7 [BRENDA, 2014, Fox76]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 15
[UniProt, 2010]
UniProt: ADP-glucose;
Sequence-Conflict 63
[Kumar86, UniProt, 2010]
Alternate sequence: F → S; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 102 -> 103
[Kumar86, UniProt, 2010]
Alternate sequence: AY → VH; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 245
[Kumar86, UniProt, 2010]
Alternate sequence: L → P; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 280
[Kumar86, UniProt, 2010]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 286
[Kumar86, UniProt, 2010]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 309
[Kumar86, UniProt, 2010]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 314
[Kumar86, UniProt, 2010]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 317 -> 318
[Kumar86, UniProt, 2010]
Alternate sequence: LL → SS; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 387
[Kumar86, UniProt, 2010]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 419
[Kumar86, UniProt, 2010]
Alternate sequence: S → N; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 422
[Kumar86, UniProt, 2010]
Alternate sequence: V → I; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 434
[Kumar86, UniProt, 2010]
Alternate sequence: A → T; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 444
[Kumar86, UniProt, 2010]
Alternate sequence: R → C; UniProt: (in Ref. 1);
Sequence-Conflict 446
[Kumar86, UniProt, 2010]
Alternate sequence: S → P; UniProt: (in Ref. 1);
Sequence-Conflict 461
[Kumar86, UniProt, 2010]
Alternate sequence: S → G; UniProt: (in Ref. 1; AAA23870);
Sequence-Conflict 476
[Kumar86, UniProt, 2010]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA23870);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3429 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10377; 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

BeckerHapak95: Becker-Hapak M, Eisenstark A (1995). "Role of rpoS in the regulation of glutathione oxidoreductase (gor) in Escherichia coli." FEMS Microbiol Lett 134(1);39-44. PMID: 8593953

BolanosGarcia06: Bolanos-Garcia VM, Davies OR (2006). "Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography." Biochim Biophys Acta 1760(9);1304-13. PMID: 16814929

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

Cid02: Cid E, Geremia RA, Guinovart JJ, Ferrer JC (2002). "Glycogen synthase: towards a minimum catalytic unit?." FEBS Lett 528(1-3);5-11. PMID: 12297270

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

Fox76: Fox J, Kawaguchi K, Greenberg E, Preiss J (1976). "Biosynthesis of bacterial glycogen. Purification and properties of the Escherichia coli B ADPglucose:1,4-alpha-D-glucan 4-alpha-glucosyltransferase." Biochemistry 1976;15(4);849-57. PMID: 2288

Furukawa90: Furukawa K, Tagaya M, Inouye M, Preiss J, Fukui T (1990). "Identification of lysine 15 at the active site in Escherichia coli glycogen synthase. Conservation of Lys-X-Gly-Gly sequence in the bacterial and mammalian enzymes." J Biol Chem 265(4);2086-90. PMID: 2105316

Furukawa93a: Furukawa K, Tagaya M, Tanizawa K, Fukui T (1993). "Role of the conserved Lys-X-Gly-Gly sequence at the ADP-glucose-binding site in Escherichia coli glycogen synthase." J Biol Chem 268(32);23837-42. PMID: 8226921

Furukawa94: Furukawa K, Tagaya M, Tanizawa K, Fukui T (1994). "Identification of Lys277 at the active site of Escherichia coli glycogen synthase. Application of affinity labeling combined with site-directed mutagenesis." J Biol Chem 269(2);868-71. PMID: 8288640

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Kumar86: Kumar A, Larsen CE, Preiss J (1986). "Biosynthesis of bacterial glycogen. Primary structure of Escherichia coli ADP-glucose:alpha-1,4-glucan, 4-glucosyltransferase as deduced from the nucleotide sequence of the glgA gene." J Biol Chem 261(34);16256-9. PMID: 3097003

Montero10: Montero M, Almagro G, Eydallin G, Viale AM, Munoz FJ, Bahaji A, Li J, Rahimpour M, Baroja-Fernandez E, Pozueta-Romero J (2010). "Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression." Biochem J 433(1);107-17. PMID: 21029047

MoranZorzano07: Moran-Zorzano MT, Alonso-Casajus N, Munoz FJ, Viale AM, Baroja-Fernandez E, Eydallin G, Pozueta-Romero J (2007). "Occurrence of more than one important source of ADPglucose linked to glycogen biosynthesis in Escherichia coli and Salmonella." FEBS Lett 581(23);4423-9. PMID: 17719035

Romeo88: Romeo T, Kumar A, Preiss J (1988). "Analysis of the Escherichia coli glycogen gene cluster suggests that catabolic enzymes are encoded among the biosynthetic genes." Gene 70(2);363-76. PMID: 2975249

Romeo89: Romeo T, Preiss J (1989). "Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5'-diphosphate 3'-diphosphate and analysis of in vivo transcripts." J Bacteriol 171(5);2773-82. PMID: 2468650

Sheng09: Sheng F, Jia X, Yep A, Preiss J, Geiger JH (2009). "The crystal structures of the open and catalytically competent closed conformation of Escherichia coli glycogen synthase." J Biol Chem 284(26);17796-807. PMID: 19244233

Sheng09a: Sheng F, Yep A, Feng L, Preiss J, Geiger JH (2009). "Oligosaccharide binding in Escherichia coli glycogen synthase." Biochemistry 48(42);10089-97. PMID: 19761218

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

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Yang96: Yang H, Liu MY, Romeo T (1996). "Coordinate genetic regulation of glycogen catabolism and biosynthesis in Escherichia coli via the CsrA gene product." J Bacteriol 178(4);1012-7. PMID: 8576033

Yep04: Yep A, Ballicora MA, Sivak MN, Preiss J (2004). "Identification and characterization of a critical region in the glycogen synthase from Escherichia coli." J Biol Chem 279(9);8359-67. PMID: 14665620

Yep04a: Yep A, Ballicora MA, Preiss J (2004). "The active site of the Escherichia coli glycogen synthase is similar to the active site of retaining GT-B glycosyltransferases." Biochem Biophys Res Commun 316(3);960-6. PMID: 15033495

Yep06: Yep A, Ballicora MA, Preiss J (2006). "The ADP-glucose binding site of the Escherichia coli glycogen synthase." Arch Biochem Biophys 453(2);188-96. PMID: 16919233

Other References Related to Gene Regulation

Baker02: Baker CS, Morozov I, Suzuki K, Romeo T, Babitzke P (2002). "CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli." Mol Microbiol 44(6);1599-610. PMID: 12067347

Bridger78: Bridger WA, Paranchych W (1978). "relA Gene control of bacterial glycogen synthesis." Can J Biochem 56(6);403-6. PMID: 352487

MedinaRivera11: Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J (2011). "Theoretical and empirical quality assessment of transcription factor-binding motifs." Nucleic Acids Res 39(3);808-24. PMID: 20923783

Montero09: Montero M, Eydallin G, Viale AM, Almagro G, Munoz FJ, Rahimpour M, Sesma MT, Baroja-Fernandez E, Pozueta-Romero J (2009). "Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes." Biochem J 424(1);129-41. PMID: 19702577

Traxler08: Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, Smith JT, Conway T (2008). "The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli." Mol Microbiol 68(5);1128-48. PMID: 18430135


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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 Sat Nov 22, 2014, biocyc13.