Escherichia coli K-12 substr. MG1655 Enzyme: glyceraldehyde 3-phosphate dehydrogenase

Gene: gapA Accession Numbers: EG10367 (EcoCyc), b1779, ECK1777

Synonyms: gad, gap1, GAPDH-A

Regulation Summary Diagram: ?

Regulation summary diagram for gapA

Subunit composition of glyceraldehyde 3-phosphate dehydrogenase = [GapA]4
         glyceraldehyde 3-phosphate dehydrogenase-A monomer = GapA

Glyceraldehyde 3-phosphate dehydrogenase A catalyzes the reversible oxidative phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-bisphospho-D-glycerate in the presence of NAD+ and phosphate during glycolysis and gluconeogenesis in E. coli. The enzyme is also found in many other organisms and its properties have been extensively studied (see [ENZYMESVOLXIII76]).

E. coli is unusual in having two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activities encoded by gapA and epd (gapB). However, the gapA encoded enzyme has a highly efficient phosphorylating glyceraldehyde-3-phosphate dehydrogenase activity and a low phosphorylating erythrose-4-phosphate dehydrogenase activity, whereas the epd encoded enzyme has an efficient non-phosphorylating erythrose-4-phosphate dehydrogenase activity and a very low phosphorylating glyceraldehyde-3-phosphate dehydrogenase activity [Zhao95, BoschiMuller97].

The GapA protein has a sequence that is more similar to eukaryotic sequences than to the thermophilic bacterial enzymes, and to prokaryotic enzymes in general [Doolittle90, Branlant85]. The gapA product is required for glycolysis, while the epd product is not [Seta97]. Both enzymes may be involved in production of pyridoxal 5'-phosphate (PLP) [Yang98].

Early studies of gapA mutants from E. coli K-10 implicated its role in glycolysis and demonstrated some of its catalytic properties [Hillman75, Hillman79]. A gapA mutant exhibits a growth defect and also exhibits increased aggregation and lysis phenotypes that are rescued by high-salt media [Seta97].

Regulation of gapA gene expression has been studied [Charpentier94, Charpentier98, Riehle03, Thouvenot04]. The regulation of the fkpA, gapA, and hslT genes is affected by evolution under conditions of chronic heat stress [Riehle03].

The E.coli sequence contains several amino acids that are conserved in all GAPDHs and are postulated to be involved NAD+ binding, or the catalytic mechanism [Branlant85, Soukri89].

The crystal structure of the wild-type enzyme in the presence of NAD+ has been determined at 1.80 Å resolution and was similar to those of other GAPDHs. The crystal structure of a N313T mutant was also determined at 2.17 Å resolution [Duee96]. Several other E. coli GAPDH crystal structures have been reported with and without bound NAD+, and in the hemiacetal intermediate state [Yun00].

Molecular factors responsible for the NAD+ cofactor stereospecificity have been studied using site-directed mutagenesis. The enzyme is a B-specific dehydrogenase that catalyzes transfer of the pro-S hydrogen and binds NAD(H) in the syn nicotinamide orientation [Eyschen99]. Refolding of denatured E. coli GAPDH in the presence of chaperone protein Tig; trigger factor has been studied [Huang00].

ADP-ribosylated GAPDH is a secreted virulence factor in some fungi and Gram-positive pathogens, as well as in pathogenic strains of E. coli. Non-pathogenic E. coli do not secrete GAPDH [Egea07, Aguilera09]. Evidence suggests that E. coli GAPDH is also involved in DNA repair [Ferreira, Ferreira15].

A series of vectors inducibly expressing paired-terminus antisense RNAs was constructed to silence central carbon metabolism in host E. coli K-12 MG1655. A vector that silenced gapA at 93% efficacy caused severe growth inhibition [Nakashima14]. Regulating the expression of an engineered E. coli gapA through changes in temperature has been demonstrated to control glycolysis [Cho12].

Gene Citations: [Nonaka06]

Locations: membrane, cytosol

Map Position: [1,860,795 -> 1,861,790] (40.11 centisomes, 144°)
Length: 996 bp / 331 aa

Molecular Weight of Polypeptide: 35.532 kD (from nucleotide sequence), 35.0 kD (experimental) [DAlessio71a ]

Molecular Weight of Multimer: 144.0 kD (experimental) [DAlessio71]

pI: 7.07

Isozyme Sequence Similarity:
Epd: YES

Unification Links: ASAP:ABE-0005920 , DIP:DIP-31848N , EchoBASE:EB0362 , EcoGene:EG10367 , EcoliWiki:b1779 , Mint:MINT-1255410 , OU-Microarray:b1779 , PortEco:gapA , PR:PRO_000022749 , Pride:P0A9B2 , Protein Model Portal:P0A9B2 , RefSeq:NP_416293 , RegulonDB:EG10367 , SMR:P0A9B2 , String:511145.b1779 , UniProt:P0A9B2

Relationship Links: InterPro:IN-FAMILY:IPR006424 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR020828 , InterPro:IN-FAMILY:IPR020829 , InterPro:IN-FAMILY:IPR020830 , InterPro:IN-FAMILY:IPR020831 , Panther:IN-FAMILY:PTHR10836 , PDB:Structure:1DC3 , PDB:Structure:1DC4 , PDB:Structure:1DC5 , PDB:Structure:1DC6 , PDB:Structure:1GAD , PDB:Structure:1GAE , PDB:Structure:1S7C , PDB:Structure:2VYN , PDB:Structure:2VYV , Pfam:IN-FAMILY:PF00044 , Pfam:IN-FAMILY:PF02800 , Prints:IN-FAMILY:PR00078 , Prosite:IN-FAMILY:PS00071 , Smart:IN-FAMILY:SM00846

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for gapA

GO Terms:

Biological Process: GO:0006096 - glycolytic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Seta97]
GO:0006006 - glucose metabolic process Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0004365 - glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Inferred from experiment Inferred by computational analysis [GOA01, Eyschen99]
GO:0051287 - NAD binding Inferred from experiment Inferred by computational analysis [GOA01a, Eyschen99]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0050661 - NADP binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05, Bairoch93, Lasserre06, Branlant85]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers pyridoxal 5'phosphate
metabolism central intermediary metabolism
metabolism energy metabolism, carbon glycolysis

Essentiality data for gapA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Last-Curated ? 04-Mar-2015 by Fulcher C , SRI International

Enzymatic reaction of: glyceraldehyde 3-phosphate dehydrogenase

Synonyms: GAPDH, triosephosphate dehydrogenase

EC Number:

D-glyceraldehyde 3-phosphate + NAD+ + phosphate <=> 1,3-bisphospho-D-glycerate + NADH + H+

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.

This reaction is reversible. [Soukri89]

In Pathways: superpathway of hexitol degradation (bacteria) , superpathway of glycolysis and Entner-Doudoroff , superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , gluconeogenesis I , glycolysis II (from fructose 6-phosphate) , glycolysis I (from glucose 6-phosphate)

The pH optimum was 8.8 in sodium pyrophosphate buffer, and 8.0 in Tris-chloride or triethanolamine-chloride buffer [DAlessio71a]. The enzyme shows esterase activity with p-nitrophenyl acetate as substrate. The esterase activity is inhibited by AMP, ADP and ATP [DAlessio71a].

The enzyme is inhibited by various dihydropyrazine derivatives and the inhibition can be reversed by several sulfhydryl compounds [Takechi10].

Cofactor Binding Comment: GAPDH has a high affinity for its cofactor NAD+. NAD+ is an essential requirement for both catalytic functions (phosphorylative activity and oxidative activity) Although NAD+ is not itself a reactant, its binding apparently effects a conformational change necessary for activity of the phosphorylative head.[Hillman79]

Activators (Unknown Mechanism): arsenate [Zhao95]

Inhibitors (Unknown Mechanism): iodoacetate [DAlessio71a]

Kinetic Parameters:

Km (μM)
D-glyceraldehyde 3-phosphate
[Eyschen99, BRENDA14]
[Eyschen99, BRENDA14]
[Eyschen99, BRENDA14]

pH(opt): 8.8 [BRENDA14]

Sequence Features

Protein sequence of glyceraldehyde 3-phosphate dehydrogenase-A monomer with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Pasquali94, Link97, UniProt12]
UniProt: Removed.
Chain 2 -> 331
UniProt: Glyceraldehyde-3-phosphate dehydrogenase A;
Nucleotide-Phosphate-Binding-Region 12 -> 13
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 34
[Yun00, UniProt15]
UniProt: NAD.
Extrinsic-Sequence-Variant 43
UniProt: In strain: ECOR 70..
Amino-Acid-Sites-That-Bind 78
[Yun00, UniProt15]
UniProt: NAD; via carbonyl oxygen.
N6-succinyllysine-Modification 115
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 124
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
N6-acetyllysine-Modification 132
[Zhang09, UniProt15]
UniProt: N6-acetyllysine; alternate.
N6-succinyllysine-Modification 132
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine; alternate.
N6-acetyllysine-Modification 138
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Protein-Segment 149 -> 151
UniProt: Glyceraldehyde 3-phosphate binding; Sequence Annotation Type: region of interest;
Active-Site 150
UniProt: Nucleophile.
Amino-Acid-Site 177
UniProt: Activates thiol group during catalysis; Sequence Annotation Type: site.
Mutagenesis-Variant 177
[Soukri89, UniProt11]
UniProt: Reduces activity about 50-fold.
Amino-Acid-Sites-That-Bind 180
[Yun00, UniProt15]
UniProt: Glyceraldehyde 3-phosphate.
Acetylation-Modification 184
N6-acetyllysine-Modification 192
[Zhang09, UniProt15]
UniProt: N6-acetyllysine; alternate.
N6-succinyllysine-Modification 192
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine; alternate.
Protein-Segment 209 -> 210
UniProt: Glyceraldehyde 3-phosphate binding; Sequence Annotation Type: region of interest;
N6-succinyllysine-Modification 213
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 217
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 225
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
Amino-Acid-Sites-That-Bind 232
[Yun00, UniProt15]
UniProt: Glyceraldehyde 3-phosphate.
N6-acetyllysine-Modification 249
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
N6-succinyllysine-Modification 249
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 257
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 261
[Zhang11c, UniProt12a]
UniProt: N6-succinyllysine.
Extrinsic-Sequence-Variant 266
UniProt: In strain: E830587..
Extrinsic-Sequence-Variant 267
UniProt: In strain: E2666-74..
Amino-Acid-Sites-That-Bind 314
[Yun00, UniProt15]
UniProt: NAD.
N6-succinyllysine-Modification 331
[Zhang11c, UniProt15]
UniProt: N6-succinyllysine; alternate.
Modified-Residue 331
[Peng11, UniProt12a]
UniProt: N6-malonyllysine; alternate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1779 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10367; confirmed by SwissProt match.


Aguilera09: Aguilera L, Gimenez R, Badia J, Aguilar J, Baldoma L (2009). "NAD+-dependent post-translational modification of Escherichia coli glyceraldehyde-3-phosphate dehydrogenase." Int Microbiol 12(3);187-92. PMID: 19784925

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

Bairoch93: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

BoschiMuller97: Boschi-Muller S, Azza S, Pollastro D, Corbier C, Branlant G (1997). "Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase." J Biol Chem 272(24);15106-12. PMID: 9182530

Branlant85: Branlant G, Branlant C (1985). "Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase." Eur J Biochem 1985;150(1);61-6. PMID: 2990926

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Charpentier94: Charpentier B, Branlant C (1994). "The Escherichia coli gapA gene is transcribed by the vegetative RNA polymerase holoenzyme E sigma 70 and by the heat shock RNA polymerase E sigma 32." J Bacteriol 1994;176(3);830-9. PMID: 8300536

Charpentier98: Charpentier B, Bardey V, Robas N, Branlant C (1998). "The EIIGlc protein is involved in glucose-mediated activation of Escherichia coli gapA and gapB-pgk transcription." J Bacteriol 1998;180(24);6476-83. PMID: 9851989

Cho12: Cho HS, Seo SW, Kim YM, Jung GY, Park JM (2012). "Engineering glyceraldehyde-3-phosphate dehydrogenase for switching control of glycolysis in Escherichia coli." Biotechnol Bioeng 109(10);2612-9. PMID: 22528318

DAlessio71: D'Alessio G, Josse J (1971). "Glyceraldehyde phosphate dehydrogenase, phosphoglycerate kinase, and phosphoglyceromutase of Escherichia coli. Simultaneous purification and physical properties." J Biol Chem 1971;246(13);4319-25. PMID: 4932978

DAlessio71a: D'Alessio G, Josse J (1971). "Glyceraldehyde phosphate dehydrogenase of Escherichia coli. Structural and catalytic properties." J Biol Chem 246(13);4326-33. PMID: 4326214

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

Doolittle90: Doolittle RF, Feng DF, Anderson KL, Alberro MR (1990). "A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote." J Mol Evol 1990;31(5);383-8. PMID: 2124629

Duee96: Duee E, Olivier-Deyris L, Fanchon E, Corbier C, Branlant G, Dideberg O (1996). "Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: implication for NAD binding and cooperativity." J Mol Biol 257(4);814-38. PMID: 8636984

Egea07: Egea L, Aguilera L, Gimenez R, Sorolla MA, Aguilar J, Badia J, Baldoma L (2007). "Role of secreted glyceraldehyde-3-phosphate dehydrogenase in the infection mechanism of enterohemorrhagic and enteropathogenic Escherichia coli: interaction of the extracellular enzyme with human plasminogen and fibrinogen." Int J Biochem Cell Biol 39(6);1190-203. PMID: 17449317

ENZYMESVOLXIII76: "Oxidation-Reduction, Part C." The Enzymes, Vol.XIII Academic Press, New York 1976;3rd Edition.

Eyschen99: Eyschen J, Vitoux B, Marraud M, Cung MT, Branlant G (1999). "Engineered glycolytic glyceraldehyde-3-phosphate dehydrogenase binds the anti conformation of NAD+ nicotinamide but does not experience A-specific hydride transfer." Arch Biochem Biophys 364(2);219-27. PMID: 10190977

Ferreira: Ferreira E, Gimenez R, Aguilera L, Guzman K, Aguilar J, Badia J, Baldoma L (2013). "Protein interaction studies point to new functions for Escherichia coli glyceraldehyde-3-phosphate dehydrogenase." Res Microbiol 164(2);145-54. PMID: 23195894

Ferreira15: Ferreira E, Gimenez R, Canas MA, Aguilera L, Aguilar J, Badia J, Baldoma L (2015). "Glyceraldehyde-3-phosphate dehydrogenase is required for efficient repair of cytotoxic DNA lesions in Escherichia coli." Int J Biochem Cell Biol 60;202-12. PMID: 25603270

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."

Hillman75: Hillman JD, Fraenkel DG (1975). "Glyceraldehyde 3-phosphate dehydrogenase mutants of Escherichia coli." J Bacteriol 122(3);1175-9. PMID: 1097392

Hillman79: Hillman JD (1979). "Mutant analysis of glyceraldehyde 3-phosphate dehydrogenase in Escherichia coli." Biochem J 1979;179(1);99-107. PMID: 89843

Huang00: Huang GC, Li ZY, Zhou JM, Fischer G (2000). "Assisted folding of D-glyceraldehyde-3-phosphate dehydrogenase by trigger factor." Protein Sci 9(6);1254-61. PMID: 10892818

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

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

Nakashima14: Nakashima N, Ohno S, Yoshikawa K, Shimizu H, Tamura T (2014). "A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli." Appl Environ Microbiol 80(2);564-73. PMID: 24212579

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Pasquali94: Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F. (1994). Data submission to UniProtKB on 1994-09.

Peng11: Peng C, Lu Z, Xie Z, Cheng Z, Chen Y, Tan M, Luo H, Zhang Y, He W, Yang K, Zwaans BM, Tishkoff D, Ho L, Lombard D, He TC, Dai J, Verdin E, Ye Y, Zhao Y (2011). "The first identification of lysine malonylation substrates and its regulatory enzyme." Mol Cell Proteomics 10(12);M111.012658. PMID: 21908771

Riehle03: Riehle MM, Bennett AF, Lenski RE, Long AD (2003). "Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature." Physiol Genomics 14(1);47-58. PMID: 12672900

Seta97: Seta FD, Boschi-Muller S, Vignais ML, Branlant G (1997). "Characterization of Escherichia coli strains with gapA and gapB genes deleted." J Bacteriol 1997;179(16);5218-21. PMID: 9260967

Shimada05: Shimada T, Fujita N, Maeda M, Ishihama A (2005). "Systematic search for the Cra-binding promoters using genomic SELEX system." Genes Cells 10(9);907-18. PMID: 16115199

Soukri89: Soukri A, Mougin A, Corbier C, Wonacott A, Branlant C, Branlant G (1989). "Role of the histidine 176 residue in glyceraldehyde-3-phosphate dehydrogenase as probed by site-directed mutagenesis." Biochemistry 28(6);2586-92. PMID: 2659073

Takechi10: Takechi S, Nakahara K, Yamaguchi T (2010). "Dihydropyrazine-induced inactivation of glyceraldehyde-3-phosphate dehydrogenase." Biol Pharm Bull 33(3);379-83. PMID: 20190396

Thouvenot04: Thouvenot B, Charpentier B, Branlant C (2004). "The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants." Biochem J 383(Pt 2);371-82. PMID: 15250823

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

UniProt12: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 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."

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

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

Yang98: Yang Y, Zhao G, Man TK, Winkler ME (1998). "Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." J Bacteriol 1998;180(16);4294-9. PMID: 9696782

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Yun00: Yun M, Park CG, Kim JY, Park HW (2000). "Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes." Biochemistry 39(35);10702-10. PMID: 10978154

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Zhang11c: Zhang Z, Tan M, Xie Z, Dai L, Chen Y, Zhao Y (2011). "Identification of lysine succinylation as a new post-translational modification." Nat Chem Biol 7(1);58-63. PMID: 21151122

Zhao95: Zhao G, Pease AJ, Bharani N, Winkler ME (1995). "Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis." J Bacteriol 1995;177(10);2804-12. PMID: 7751290

Other References Related to Gene Regulation

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

Olvera09: Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolivar F (2009). "Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation." PLoS One 4(10);e7466. PMID: 19838295

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065

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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 19.0 on Sun Jul 5, 2015, biocyc11.