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Escherichia coli K-12 substr. MG1655 Enzyme: malate synthase G



Gene: glcB Accession Numbers: EG20080 (EcoCyc), b2976, ECK2970

Synonyms: glc

Regulation Summary Diagram: ?

Summary:
There are two isozymes of malate synthase in E. coli [Falmagne65]. Malate synthase G, encoded by the glcB gene, is responsible for almost all of the malate synthase activity in cells metabolizing glyoxylate that is formed during growth on glycolate [Vanderwinkel68, Ornston69]. Malate synthase A, encoded by the aceB gene, is involved in the glyoxylate bypass. It metabolizes glyoxylate formed in the dissimilation of acetate [Molina94].

Crystal and solution structures of malate synthase G in various conformations have been determined, and a reaction mechanism has been proposed [Howard00, Tugarinov03, Anstrom03, Tugarinov05]. Active site residues were confirmed by site-directed mutagenesis [Anstrom03].

Expression of glcB is inducible by glycolate [Ornston69, Pellicer99a]; the glc operon was also shown to be inducible by acetate [Pellicer99a].

Gene Citations: [Nunez01]

Locations: cytosol

Map Position: [3,119,656 <- 3,121,827] (67.24 centisomes)
Length: 2172 bp / 723 aa

Molecular Weight of Polypeptide: 80.488 kD (from nucleotide sequence), 82 kD (experimental) [Molina94 ]

Unification Links: ASAP:ABE-0009767 , CGSC:711 , DIP:DIP-9761N , EchoBASE:EB4141 , EcoGene:EG20080 , EcoliWiki:b2976 , Mint:MINT-1248166 , ModBase:P37330 , OU-Microarray:b2976 , PortEco:glcB , PR:PRO_000022772 , Pride:P37330 , Protein Model Portal:P37330 , RefSeq:NP_417450 , RegulonDB:EG20080 , SMR:P37330 , String:511145.b2976 , UniProt:P37330

Relationship Links: InterPro:IN-FAMILY:IPR001465 , InterPro:IN-FAMILY:IPR006253 , InterPro:IN-FAMILY:IPR011076 , InterPro:IN-FAMILY:IPR023310 , Panther:IN-FAMILY:PTHR21631:SF1 , PDB:Structure:1D8C , PDB:Structure:1P7T , PDB:Structure:1Y8B , PDB:Structure:2JQX , Pfam:IN-FAMILY:PF01274

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009436 - glyoxylate catabolic process Inferred from experiment [Ornston69]
GO:0006097 - glyoxylate cycle Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a]
GO:0006099 - tricarboxylic acid cycle Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004474 - malate synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Falmagne73]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism glyoxylate degradation

Essentiality data for glcB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 11-Sep-2007 by Keseler I , SRI International


Enzymatic reaction of: malate synthase G

EC Number: 2.3.3.9

acetyl-CoA + glyoxylate + H2O <=> (S)-malate + coenzyme A + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is irreversible in the direction shown.

In Pathways: superpathway of glycol metabolism and degradation , glycolate and glyoxylate degradation II

Summary:
The Kd for glyoxylate is 600 µM [Tugarinov03].

Cofactors or Prosthetic Groups: Mg2+

Inhibitors (Competitive): oxalate [Falmagne65] , glycolate [Falmagne65]

Inhibitors (Unknown Mechanism): pyruvate [Anstrom03]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
acetyl-CoA
22.0, 9.0
[Lohman08, BRENDA14]
acetyl-CoA
9.0
[Anstrom03, BRENDA14]
glyoxylate
55.0, 21.0
[Lohman08, BRENDA14]
glyoxylate
21.0
48.1
[Anstrom03, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Falmagne73, Molina94]
 
Chain 2 -> 723
[UniProt09]
UniProt: Malate synthase G;
Amino-Acid-Sites-That-Bind 118
[UniProt14]
UniProt: Acetyl-CoA; via carbonyl oxygen.
Protein-Segment 125 -> 126
[UniProt14]
UniProt: Acetyl-CoA binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 274
[UniProt14]
UniProt: Acetyl-CoA.
Amino-Acid-Sites-That-Bind 311
[UniProt14]
UniProt: Acetyl-CoA.
Mutagenesis-Variant 338
[Anstrom03, UniProt14]
Alternate sequence: R → K; UniProt: Has a specific activity which is only 6.6% of the wild-type activity.
Amino-Acid-Sites-That-Bind 338
[UniProt14]
UniProt: Glyoxylate.
Active-Site 338
[Anstrom03, Howard00, UniProt10]
UniProt: Proton acceptor;
Metal-Binding-Site 427
[UniProt14]
UniProt: Magnesium.
Protein-Segment 452 -> 455
[UniProt14]
UniProt: Glyoxylate binding; Sequence Annotation Type: region of interest.
Metal-Binding-Site 455
[UniProt14]
UniProt: Magnesium.
Amino-Acid-Sites-That-Bind 536
[UniProt14]
UniProt: Acetyl-CoA; via carbonyl oxygen.
Mutagenesis-Variant 617
[Anstrom03, UniProt14]
Alternate sequence: C → S; UniProt: Affinity binding for acetyl-CoA is more than five times greater than that of wild-type, although its specific activity is comparable.
Cysteine-sulfenic-acid-Modification 617
[UniProt14]
UniProt: Cysteine sulfenic acid (-SOH).
Mutagenesis-Variant 631
[Anstrom03, UniProt14]
Alternate sequence: D → N; UniProt: Absence of malate synthase activity.
Active-Site 631
[Anstrom03, Howard00, UniProt10]
UniProt: Proton donor;
Cysteine-sulfenic-acid-Modification 688
[UniProt14]
UniProt: Cysteine sulfenic acid (-SOH).


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2976 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG20080; confirmed by SwissProt match.


References

Anstrom03: Anstrom DM, Kallio K, Remington SJ (2003). "Structure of the Escherichia coli malate synthase G:pyruvate:acetyl-coenzyme A abortive ternary complex at 1.95 A resolution." Protein Sci 12(9);1822-32. PMID: 12930982

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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

Falmagne65: Falmagne P, Vanderwinkel E, Wiame JM (1965). "Mise en evidence de deux malate synthases chez E. coli." BBActa 1965;99:246-258. PMID: 14336062

Falmagne73: Falmagne P, Wiame JM (1973). "[Purification and partial characterization of two malate synthases of Echerichia coli]." Eur J Biochem 37(3);415-24. PMID: 4591144

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

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."

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

Howard00: Howard BR, Endrizzi JA, Remington SJ (2000). "Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 A resolution: mechanistic implications." Biochemistry 39(11);3156-68. PMID: 10715138

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

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

Lohman08: Lohman JR, Olson AC, Remington SJ (2008). "Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery." Protein Sci 17(11);1935-45. PMID: 18714089

Molina94: Molina I, Pellicer MT, Badia J, Aguilar J, Baldoma L (1994). "Molecular characterization of Escherichia coli malate synthase G. Differentiation with the malate synthase A isoenzyme." Eur J Biochem 1994;224(2);541-8. PMID: 7925370

Nunez01: Nunez MF, Pellicer MT, Badia J, Aguilar J, Baldoma L (2001). "The gene yghK linked to the glc operon of Escherichia coli encodes a permease for glycolate that is structurally and functionally similar to L-lactate permease." Microbiology 2001;147(Pt 4);1069-77. PMID: 11283302

Ornston69: Ornston LN, Ornston MK (1969). "Regulation of glyoxylate metabolism in Escherichia coli K-12." J Bacteriol 98(3);1098-108. PMID: 4892366

Pellicer99a: Pellicer MT, Fernandez C, Badia J, Aguilar J, Lin EC, Baldom L (1999). "Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter." J Biol Chem 274(3);1745-52. PMID: 9880556

Tugarinov03: Tugarinov V, Kay LE (2003). "Quantitative NMR studies of high molecular weight proteins: application to domain orientation and ligand binding in the 723 residue enzyme malate synthase G." J Mol Biol 327(5);1121-33. PMID: 12662935

Tugarinov05: Tugarinov V, Choy WY, Orekhov VY, Kay LE (2005). "Solution NMR-derived global fold of a monomeric 82-kDa enzyme." Proc Natl Acad Sci U S A 102(3);622-7. PMID: 15637152

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.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 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."

Vanderwinkel68: Vanderwinkel E, De Vlieghere M (1968). "[Physiology and genetics of isocitritase and the malate synthases of Escherichia coli]." Eur J Biochem 5(1);81-90. PMID: 4874804

Other References Related to Gene Regulation

Gohler11: Gohler AK, Kokpinar O, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2011). "More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli." BMC Syst Biol 5(1);197. PMID: 22168595

Liu04: Liu X, De Wulf P (2004). "Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling." J Biol Chem 279(13);12588-97. PMID: 14711822

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


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 Fri Jan 30, 2015, biocyc11.