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Escherichia coli K-12 substr. MG1655 Enzyme: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase



Gene: gpmA Accession Numbers: EG11699 (EcoCyc), b0755, ECK0744

Synonyms: gpm, BPG-dependent PGAM1, PGAM 1, dPGM

Regulation Summary Diagram: ?

Subunit composition of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase = [GpmA]2
         2,3-bisphosphoglycerate-dependent phosphoglycerate mutase monomer = GpmA

Summary:
E. coli contains both a 2,3-bisphosphoglyerate-dependent (dPGM, GpmA) and a cofactor-independent (iPGM, GpmM) phosphoglycerate mutase. The dPGM enzyme has significantly higher specific activity [Fraser99a, Foster10]. Differential inhibition by vanadate allowed independent measurement of both enzymes during the E. coli growth cycle [Fraser99a].

Crystal structures of the enzyme have been solved at 1.25 Å [Bond01] and 1.25 Å [Bond02] resolution. The active site His10 residue is phosphorylated in approximately 1/4 of the polypeptides in the structure and may represent the active form of the enzyme [Bond01]. The crystal structure of the enzyme in complex with the inhibitor vanadate resembles that of the inactive dephosphorylated dPGM of Saccharomyces cerevisiae [Bond02].

A gpmA deletion strain shows a growth lag in minimal medium, which may be due to a delay in exiting stationary phase. This phenotype can be rescued by expression of either gpmA or gpmM from a medium-copy plasmid. A gpmA gpmM double mutant strain does not appear to be viable [Foster10].

Transcription of gpmA is regulated by Fur [Vassinova00].

Locations: cytosol

Map Position: [786,066 <- 786,818] (16.94 centisomes)
Length: 753 bp / 250 aa

Molecular Weight of Polypeptide: 28.556 kD (from nucleotide sequence), 27.0 kD (experimental) [Fraser99a ]

Molecular Weight of Multimer: 49.0 kD (experimental) [Fraser99a]

pI: 6.16

Unification Links: ASAP:ABE-0002563 , CGSC:35790 , DIP:DIP-35899N , EchoBASE:EB1650 , EcoGene:EG11699 , EcoliWiki:b0755 , Mint:MINT-1227975 , OU-Microarray:b0755 , PortEco:gpmA , PR:PRO_000022830 , Pride:P62707 , Protein Model Portal:P62707 , RefSeq:NP_415276 , RegulonDB:EG11699 , SMR:P62707 , String:511145.b0755 , UniProt:P62707

Relationship Links: InterPro:IN-FAMILY:IPR001345 , InterPro:IN-FAMILY:IPR005952 , InterPro:IN-FAMILY:IPR013078 , Panther:IN-FAMILY:PTHR11931 , PDB:Structure:1E58 , PDB:Structure:1E59 , Pfam:IN-FAMILY:PF00300 , Prosite:IN-FAMILY:PS00175 , Smart:IN-FAMILY:SM00855

In Paralogous Gene Group: 190 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006096 - glycolytic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0042803 - protein homodimerization activity Inferred from experiment [Fraser99a]
GO:0046538 - 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity Inferred from experiment Inferred by computational analysis [GOA06, Fraser99a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0004619 - phosphoglycerate mutase activity Inferred by computational analysis [GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

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

Essentiality data for gpmA 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]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 05-Jan-2011 by Keseler I , SRI International


Enzymatic reaction of: phosphoglycerate mutase

Synonyms: D-phosphoglycerate 2,3-phosphomutase, phosphoglycerate phosphomutase, phosphoglyceromutase

EC Number: 5.4.2.11

2-phospho-D-glycerate <=> 3-phospho-D-glycerate

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. [Fraser99a]

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

Summary:
The kcat and Km values in the forward and reverse directions have been measured [Fraser99a].

Cofactors or Prosthetic Groups: 2,3-diphospho-D-glycerate [Fraser99a]

Inhibitors (Unknown Mechanism): vanadate [Fraser99a, Foster10, Comment 4]

Kinetic Parameters:

Substrate
Km (μM)
Citations
2-phospho-D-glycerate
190.0
[Fraser99a]
3-phospho-D-glycerate
200.0
[Fraser99a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Pasquali94, Nystrom96a, Wilkins98, Link97, UniProt12]
UniProt: Removed.
Chain 2 -> 250
[UniProt09]
UniProt: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase;
Active-Site 11
[Bond01, UniProt10a]
UniProt: Tele-phosphohistidine intermediate;
Amino-Acid-Sites-That-Bind 17
[UniProt13]
UniProt: 2-phospho-D-glycerate; Non-Experimental Qualifier: probable.
Acetylation-Modification 18
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
Protein-Segment 23 -> 24
[UniProt13]
UniProt: 2-phospho-D-glycerate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: probable.
Amino-Acid-Sites-That-Bind 62
[UniProt13]
UniProt: 2-phospho-D-glycerate; Non-Experimental Qualifier: probable.
Protein-Segment 89 -> 92
[UniProt13]
UniProt: 2-phospho-D-glycerate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: probable.
Amino-Acid-Sites-That-Bind 100
[UniProt13]
UniProt: 2-phospho-D-glycerate; Non-Experimental Qualifier: probable.
Acetylation-Modification 100
[Zhang09, UniProt10a, Yu08]
UniProt: N6-acetyllysine;
Acetylation-Modification 106
[Zhang09, UniProt10a, Yu08]
UniProt: N6-acetyllysine;
Protein-Segment 116 -> 117
[UniProt13]
UniProt: 2-phospho-D-glycerate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: probable.
Active-Site 184
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 186
[UniProt13]
UniProt: 2-phospho-D-glycerate; Non-Experimental Qualifier: probable.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0755 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11699; 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

Bond01: Bond CS, White MF, Hunter WN (2001). "High resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase." J Biol Chem 276(5);3247-53. PMID: 11038361

Bond02: Bond CS, White MF, Hunter WN (2002). "Mechanistic implications for Escherichia coli cofactor-dependent phosphoglycerate mutase based on the high-resolution crystal structure of a vanadate complex." J Mol Biol 316(5);1071-81. PMID: 11884145

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

Foster10: Foster JM, Davis PJ, Raverdy S, Sibley MH, Raleigh EA, Kumar S, Carlow CK (2010). "Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers." PLoS One 5(10);e13576. PMID: 21187861

Fraser99a: Fraser HI, Kvaratskhelia M, White MF (1999). "The two analogous phosphoglycerate mutases of Escherichia coli." FEBS Lett 1999;455(3);344-8. PMID: 10437801

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, 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

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

Nystrom96a: Nystrom T, Larsson C, Gustafsson L (1996). "Bacterial defense against aging: role of the Escherichia coli ArcA regulator in gene expression, readjusted energy flux and survival during stasis." EMBO J 15(13);3219-28. PMID: 8670822

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.

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.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11: 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."

Vassinova00: Vassinova N, Kozyrev D (2000). "A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli." Microbiology 146 Pt 12;3171-82. PMID: 11101675

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

Chen07: Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD (2007). "Discovery of Fur binding site clusters in Escherichia coli by information theory models." Nucleic Acids Res 35(20);6762-77. PMID: 17921503

Durand10: Durand S, Storz G (2010). "Reprogramming of anaerobic metabolism by the FnrS small RNA." Mol Microbiol 75(5);1215-31. PMID: 20070527

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


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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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