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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Enzyme: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase



Gene: gpmM Accession Numbers: EG12296 (EcoCyc), b3612, ECK3602

Synonyms: gpmC, pgmI, gpmI, yibO

Regulation Summary Diagram: ?

Summary:
E. coli contains both a 2,3-bisphosphoglyerate-dependent (dPGM, GpmA) and a cofactor-independent (iPGM, GpmM) phosphoglycerate mutase. The iPGM enzyme has significantly lower specific activity [Fraser99, Foster10]. Differential inhibition by vanadate allowed independent measurement of both enzymes during the E. coli growth cycle [Fraser99].

A gpmM deletion strain does not have a growth defect under the conditions tested, while a gpmA gpmM double mutant strain does not appear to be viable. The growth phenotype of a gpmA mutant can be rescued by expression of gpmM from a medium-copy plasmid [Foster10].

gpmM shows differential codon adaptation, resulting in differential translation efficiency signatures, in aerotolerant compared to obligate anaerobic microbes. It was therefore predicted to play a role in the oxidative stress response. A gpmM deletion mutant was shown to be more sensitive than wild-type specifically to hydrogen peroxide exposure, but not other stresses [Krisko14].

Review: [Jedrzejas01]

Locations: cytosol

Map Position: [3,783,283 -> 3,784,827] (81.54 centisomes)
Length: 1545 bp / 514 aa

Molecular Weight of Polypeptide: 56.194 kD (from nucleotide sequence), 61.0 kD (experimental) [Fraser99 ]

Unification Links: ASAP:ABE-0011818 , DIP:DIP-12425N , EchoBASE:EB2204 , EcoGene:EG12296 , EcoliWiki:b3612 , ModBase:P37689 , OU-Microarray:b3612 , PortEco:gpmM , PR:PRO_000022831 , Pride:P37689 , Protein Model Portal:P37689 , RefSeq:NP_418069 , RegulonDB:EG12296 , SMR:P37689 , String:511145.b3612 , Swiss-Model:P37689 , UniProt:P37689

Relationship Links: InterPro:IN-FAMILY:IPR005995 , InterPro:IN-FAMILY:IPR006124 , InterPro:IN-FAMILY:IPR011258 , InterPro:IN-FAMILY:IPR017849 , InterPro:IN-FAMILY:IPR017850 , Pfam:IN-FAMILY:PF01676 , Pfam:IN-FAMILY:PF06415

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Krisko14]
GO:0006007 - glucose catabolic process Inferred by computational analysis [GOA01]
GO:0006096 - glycolytic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Fraser99]
GO:0046537 - 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity Inferred from experiment Inferred by computational analysis [GOA06, Fraser99, DAlessio71a]
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]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [GOA01, Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for gpmM 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]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 08-May-2014 by Keseler I , SRI International


Enzymatic reaction of: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase

Synonyms: iPGM, PGAM, cofactor independent, phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent, phosphoglycerate mutase, BPG-independent, BPG-independent PGAM, phosphoglyceromutase, phosphoglycerate phosphomutase, D-phosphoglycerate 2,3-phosphomutase, phosphoglycerate mutase

EC Number: 5.4.2.12

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. [Fraser99]

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 kcat and Km values in the forward and reverse directions have been measured [Fraser99].

Cofactors or Prosthetic Groups: Mn2+ [Comment 5, Fraser99, Foster10]

Kinetic Parameters:

Substrate
Km (μM)
Citations
2-phospho-D-glycerate
97.0
[Fraser99]
3-phospho-D-glycerate
210.0
[Fraser99]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 14
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 64
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Active-Site 64
[UniProt10a]
UniProt: Phosphoserine intermediate; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 403
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 407
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 444
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 445
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 463
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3612 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12296; 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

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

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

Fraser99: 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

Jedrzejas01: Jedrzejas MJ, Setlow P (2001). "Comparison of the binuclear metalloenzymes diphosphoglycerate-independent phosphoglycerate mutase and alkaline phosphatase: their mechanism of catalysis via a phosphoserine intermediate." Chem Rev 101(3);607-18. PMID: 11712498

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Krisko14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

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

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

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

Other References Related to Gene Regulation

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Shimada11: Shimada T, Yamamoto K, Ishihama A (2011). "Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli." J Bacteriol 193(3);649-59. PMID: 21115656


Report Errors or Provide Feedback
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 18.5 on Mon Dec 22, 2014, biocyc13.