Escherichia coli K-12 substr. MG1655 Enzyme: phosphoglycerate kinase

Gene: pgk Accession Numbers: EG10703 (EcoCyc), b2926, ECK2922

Regulation Summary Diagram: ?

Regulation summary diagram for pgk

Phosphoglycerate kinase encoded by gene pgk catalyzes the reversible phosphorylation of 3-phospho-D-glycerate to 1,3-bisphospho-D-glycerate during glycolysis and gluconeogenesis in E. coli. In the glycolytic reaction direction the enzyme catalyzes the transfer of a phosphoryl group from 1,3-bisphospho-D-glycerate to ADP, forming ATP and 3-phospho-D-glycerate.

Pgk cDNAs from a variety of organisms have been isolated. Their protein products are all monomers of similar size, with similar tertiary structures [Fifis78, Watson90]. The amino acid sequence of the E. coli enzyme is highly homologous to that of eukaryotes [Alefounder89]. Part of gene pgk showed similarity to an ORF found in the enterobacterial fish pathogen Edwardsiella ictaluri [Moore02]. The gene order around pgk in the Enterobacteriaceae differs from that in most other bacteria and transcriptional regulation of the E. coli epd-pgk-fbaA region has been studied [Bardey05].

In earlier work, phosphoglycerate kinase was purified to near homogeneity from cell extracts of E. coli K-12. When assayed in the reverse direction its activity was dependent upon the presence of ATP and 3-phospho-D-glycerate [DAlessio71a, DAlession75, Fifis78]. A pgk mutant cannot grow on sugars or gluconeogenic substrates [Irani74, Thomson79]. A mapping study using transductional crosses determined a gene order in the pgk region [Irani76]. Pgk synthesis was shown to be induced over 10-fold during the transition from exponential to stationary growth phase. The position of the protein on two-dimensional gels indicated that it is one of the proteins induced by anaerobiosis [Nellemann89].

The crystal structure of E. coli K-12 Pgk has been determined at 2.40 Å resolution and compared with that of yeast. Both enzymes have very similar tertiary structures and measured global stabilities. Although E. coli Pgk shows 39% homology and 56% similarity with that of yeast, the E. coli enzyme is more resistant to proteolysis. Pgk consists of N and C domains that are connected by an α-helical linker. Biophyscal studies suggested that cooperativity between the N and C domains of E. coli Pgk results in more rigidity and is the basis of the increased stability [Young07]. A novel use of the N-domain of E. coli Pgk as a fusion partner to express heterologous proteins that are prone to aggregation has also been reported [Song12].

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 pgk at 79% efficacy did not cause severe growth inhibition, possibly due to residual activity [Nakashima14].

Co-overexpression of several genes including pgk in an engineered E. coli strain was a strategy for improving polyhydroxybutyrate production in an E. coli host [Zhang14c].

Gene Citations: [Charpentier98]

Locations: cytosol

Map Position: [3,069,481 <- 3,070,644] (66.16 centisomes, 238°)
Length: 1164 bp / 387 aa

Molecular Weight of Polypeptide: 41.118 kD (from nucleotide sequence), 43.7 kD (experimental) [DAlessio71a ]

Unification Links: ASAP:ABE-0009605 , CGSC:408 , DIP:DIP-36163N , EchoBASE:EB0697 , EcoGene:EG10703 , EcoliWiki:b2926 , Mint:MINT-1229247 , OU-Microarray:b2926 , PortEco:pgk , PR:PRO_000023523 , Pride:P0A799 , Protein Model Portal:P0A799 , RefSeq:NP_417401 , RegulonDB:EG10703 , SMR:P0A799 , String:511145.b2926 , Swiss-Model:P0A799 , UniProt:P0A799

Relationship Links: InterPro:IN-FAMILY:IPR001576 , InterPro:IN-FAMILY:IPR015824 , InterPro:IN-FAMILY:IPR015901 , InterPro:IN-FAMILY:IPR015911 , Panther:IN-FAMILY:PTHR11406 , PDB:Structure:1ZMR , Pfam:IN-FAMILY:PF00162 , Prints:IN-FAMILY:PR00477 , Prosite:IN-FAMILY:PS00111

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for pgk

GO Terms:

Biological Process: GO:0006096 - glycolytic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01, Irani74, DAlessio71a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004618 - phosphoglycerate kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, DAlessio71a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: metabolism central intermediary metabolism
metabolism energy metabolism, carbon glycolysis

Essentiality data for pgk knockouts: ?

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

Last-Curated ? 27-Feb-2015 by Fulcher C , SRI International

Enzymatic reaction of: phosphoglycerate kinase

Synonyms: 3-phosphoglycerate kinase, Glycerate 3-P kinase, 2,3-diphospho-D-glycerate, 2-phospho-D-glycerate phosphotransferase

EC Number:

3-phospho-D-glycerate + ATP <=> 1,3-bisphospho-D-glycerate + ADP

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. [DAlessio71a]

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)

MgATP is the phosphate donor in for 3-phospho-D-glycerate [Fifis78].

Cofactors or Prosthetic Groups: Mg2+ [Fifis78]

Sequence Features

Protein sequence of phosphoglycerate kinase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Frutiger96, Wilkins98, Link97, UniProt12]
UniProt: Removed.
Chain 2 -> 387
UniProt: Phosphoglycerate kinase;
Protein-Segment 21 -> 23
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 36
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Protein-Segment 59 -> 62
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
N6-acetyllysine-Modification 84
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Amino-Acid-Sites-That-Bind 113
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Acetylation-Modification 116
Amino-Acid-Sites-That-Bind 146
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 197
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 314
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 340 -> 343
UniProt: ATP; Non-Experimental Qualifier: by similarity;

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

Transcription-unit diagram


10/20/97 Gene b2926 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10703; confirmed by SwissProt match.


Alefounder89: Alefounder PR, Perham RN (1989). "Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli." Mol Microbiol 3(6);723-32. PMID: 2546007

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

Bardey05: Bardey V, Vallet C, Robas N, Charpentier B, Thouvenot B, Mougin A, Hajnsdorf E, Regnier P, Springer M, Branlant C (2005). "Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli." Mol Microbiol 57(5);1265-87. PMID: 16102000

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

DAlessio71a: 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

DAlession75: D'Alession G, Josse J (1975). "Phosphoglycerate kinase and phosphoglyceromutase from Escherichia coli." Methods Enzymol 42;139-44. PMID: 166274

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

Fifis78: Fifis T, Scopes RK (1978). "Purification of 3-phosphoglycerate kinase from diverse sources by affinity elution chromatography." Biochem J 175(1);311-9. PMID: 367367

Frutiger96: Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. (1996). Data submission to UniProtKB on 1996-02.

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.

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

Irani74: Irani M, Maitra PK (1974). "Isolation and characterization of Escherichia coli mutants defective in enzymes of glycolysis." Biochem Biophys Res Commun 56(1);127-33. PMID: 4595969

Irani76: Irani MH, Maitra PK (1976). "Glyceraldehyde 3-p dehydrogenase, glycerate 3-P kinase and enolase mutants of Escherichia coli: genetic studies." Mol Gen Genet 1976;145(1);65-71. PMID: 775311

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

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

Moore02: Moore MM, Fernandez DL, Thune RL (2002). "Cloning and characterization of Edwardsiella ictaluri proteins expressed and recognized by the channel catfish Ictalurus punctatus immune response during infection." Dis Aquat Organ 52(2);93-107. PMID: 12542086

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

Nellemann89: Nellemann LJ, Holm F, Atlung T, Hansen FG (1989). "Cloning and characterization of the Escherichia coli phosphoglycerate kinase (pgk) gene." Gene 1989;77(1);185-91. PMID: 2545537

Song12: Song JA, Lee DS, Park JS, Han KY, Lee J (2012). "The N-domain of Escherichia coli phosphoglycerate kinase is a novel fusion partner to express aggregation-prone heterologous proteins." Biotechnol Bioeng 109(2);325-35. PMID: 21882174

Thomson79: Thomson J, Gerstenberger PD, Goldberg DE, Gociar E, Orozco de Silva A, Fraenkel DG (1979). "ColE1 hybrid plasmids for Escherichia coli genes of glycolysis and the hexose monophosphate shunt." J Bacteriol 1979;137(1);502-6. PMID: 368027

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.

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

Watson90: Watson HC, Littlechild JA (1990). "Isoenzymes of phosphoglycerate kinase: evolutionary conservation of the structure of this glycolytic enzyme." Biochem Soc Trans 1990;18(2);187-90. PMID: 2379683

Wilkins98: Wilkins MR, Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA, Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF (1998). "Protein identification with N and C-terminal sequence tags in proteome projects." J Mol Biol 278(3);599-608. PMID: 9600841

Young07: Young TA, Skordalakes E, Marqusee S (2007). "Comparison of proteolytic susceptibility in phosphoglycerate kinases from yeast and E. coli: modulation of conformational ensembles without altering structure or stability." J Mol Biol 368(5);1438-47. PMID: 17397866

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

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

Zhang14c: Zhang Y, Lin Z, Liu Q, Li Y, Wang Z, Ma H, Chen T, Zhao X (2014). "Engineering of Serine-Deamination pathway, Entner-Doudoroff pathway and pyruvate dehydrogenase complex to improve poly(3-hydroxybutyrate) production in Escherichia coli." Microb Cell Fact 13(1);172. PMID: 25510247

Other References Related to Gene Regulation

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

Ramseier95: Ramseier TM, Bledig S, Michotey V, Feghali R, Saier MH (1995). "The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli." Mol Microbiol 1995;16(6);1157-69. PMID: 8577250

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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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