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BioCyc websites down
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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: ?

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

Summary:
E. coli is unusual in having two glyceraldehyde-3-phosphate dehydrogenases. The protein GAPDH-A has a sequence that is more similar to eukaryotic sequences than it is to the thermophilic bacterial enzymes and prokaryotic enzymes in general [Doolittle90, Branlant85]. GapA is required for glycolysis, while Epd (GapB) is not [Seta97]. GapA and Epd may be involved in production of pyridoxal 5'-phosphate (PLP) [Yang98a].

A gapA mutant exhibits a growth defect and also exhibits increased aggregation and lysis phenotypes that are rescued by high-salt media [Seta97].

Regulation has been described [Riehle03]. The regulation of the fkpA, gapA, and hslT genes is affected by evolution under conditions of chronic heat stress [Riehle03].

Gene Citations: [Nonaka06]

Locations: membrane, cytosol

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

Molecular Weight of Polypeptide: 35.532 kD (from nucleotide sequence)

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: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006006 - glucose metabolic process Inferred by computational analysis [GOA01a]
GO:0006096 - glycolytic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004365 - glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
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]
GO:0051287 - NAD 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 [UniProtGOA11, UniProtGOA11a]

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]

Enzymatic reaction of: glyceraldehyde 3-phosphate dehydrogenase

Synonyms: GAPDH, triosephosphate dehydrogenase

EC Number: 1.2.1.12

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.

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-6P) , glycolysis I (from glucose-6P)

Summary:
The E.coli sequence contains a certain number of amino acids which are conserved in all GAPDHs so far sequenced and which are postulated to be directly implicated in the NAD+ binding or in the catalysis mechanism. [Branlant85] There appear to be only two active sites per molecule.[Hillman79] NAD required for the phosphorylation as well as the oxidation [Hillman79]

Citations: [ENZYMESVOLXIII76, Seta97]

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]

Kinetic Parameters:

Substrate
Km (μM)
Citations
D-glyceraldehyde 3-phosphate
890.0
[Eyschen99, BRENDA14]
phosphate
530.0
[Eyschen99, BRENDA14]
NAD+
45.0
[Eyschen99, BRENDA14]

pH(opt): 8 [BRENDA14, DAlessio71a], 8.8 [BRENDA14, DAlessio71a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Pasquali94, Link97, UniProt12a]
UniProt: Removed.
Chain 2 -> 331
[UniProt09]
UniProt: Glyceraldehyde-3-phosphate dehydrogenase A;
Nucleotide-Phosphate-Binding-Region 12 -> 13
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 34
[UniProt10]
UniProt: NAD;
Extrinsic-Sequence-Variant 43
[UniProt10]
Alternate sequence: Y → I; UniProt: (in strain: ECOR 70);
Amino-Acid-Sites-That-Bind 78
[UniProt10]
UniProt: NAD; via carbonyl oxygen;
N6-succinyllysine-Modification 115
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 124
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 132
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine; alternate.
Acetylation-Modification 132
[Zhang09, UniProt12]
UniProt: N6-acetyllysine; alternate.
Acetylation-Modification 138
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
Protein-Segment 149 -> 151
[UniProt10a]
UniProt: Glyceraldehyde 3-phosphate binding; Sequence Annotation Type: region of interest;
Active-Site 150
[UniProt10]
UniProt: Nucleophile;
Mutagenesis-Variant 177
[Soukri89, UniProt11]
Alternate sequence: H → N; UniProt: Reduces activity about 50-fold.
Amino-Acid-Site 177
[UniProt10]
UniProt: Activates thiol group during catalysis; Sequence Annotation Type: site;
Amino-Acid-Sites-That-Bind 180
[UniProt10]
UniProt: Glyceraldehyde 3-phosphate;
Acetylation-Modification 184
[Yu08]
 
N6-succinyllysine-Modification 192
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine; alternate.
Acetylation-Modification 192
[Zhang09, UniProt12]
UniProt: N6-acetyllysine; alternate.
Protein-Segment 209 -> 210
[UniProt10a]
UniProt: Glyceraldehyde 3-phosphate binding; Sequence Annotation Type: region of interest;
N6-succinyllysine-Modification 213
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 217
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 225
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
Amino-Acid-Sites-That-Bind 232
[UniProt10]
UniProt: Glyceraldehyde 3-phosphate;
N6-succinyllysine-Modification 249
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
Acetylation-Modification 249
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
N6-succinyllysine-Modification 257
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 261
[Zhang11a, UniProt12]
UniProt: N6-succinyllysine.
Extrinsic-Sequence-Variant 266
[UniProt10]
Alternate sequence: G → D; UniProt: (in strain: E830587);
Extrinsic-Sequence-Variant 267
[UniProt10]
Alternate sequence: E → A; UniProt: (in strain: E2666-74);
Amino-Acid-Sites-That-Bind 314
[UniProt10]
UniProt: NAD;
N6-succinyllysine-Modification 331
[Peng11, Zhang11a, UniProt12]
UniProt: N6-succinyllysine; alternate.
Modified-Residue 331
[Peng11, UniProt12]
UniProt: N6-malonyllysine; alternate.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1779 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10367; 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

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

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." http://www.brenda-enzymes.org.

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

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

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."

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

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

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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 2012-09 released on 2012-09-12 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

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

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."

Yang98a: 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

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

Zhang11a: 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

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

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

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

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
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