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 is one of the proteins induced by anaerobiosis. [Nellemann89] The gene is transcribed from two promoters, one immediately in front of an upstream gene coding for a 38-kDa polypeptide of unknown function. The pgk gene was also found to show growth phase regulation. A structural determinant for glycerate 3-P kinase is located near serA. The map order is speB-pgk-serA-lysA-argA-eno-cysC.[Irani76]

Pgk has similarity to an Edwardsiella ictaluri protein [Moore02].

Gene Citations: [Alefounder89a, Bardey05, 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)

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, DAlessio71]
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, DAlessio71]
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]

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.

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 structure of Pgk determined crystallographically is best described as an open bi-lobal molecule. The active site of the enzyme lies deep in the cleft formed between the two lobes.[Watson90] When purified enzymes were employed there was absolute dependence upon the respective substrates of the glycolytic pathway. There was no activity unless ATP and glycerate-3-P were both included.[DAlessio71]

Activators (Unknown Mechanism): ATP , 3-phospho-D-glycerate

Sequence Features

Protein sequence of phosphoglycerate kinase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Frutiger96, Wilkins98, Link97, UniProt12b]
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.


Alefounder89a: 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

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

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

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."

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

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12b: 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

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

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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