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Escherichia coli K-12 substr. MG1655 Enzyme: malate dehydrogenase



Gene: maeB Accession Numbers: G7293 (EcoCyc), b2463, ECK2458

Synonyms: ypfF

Regulation Summary Diagram: ?

Subunit composition of malate dehydrogenase = [MaeB]6

Summary:
There are two malic enzymes in E. coli, one NADP-dependent (MaeB, described here) and the other NAD-dependent (encoded by the maeA gene) [Takeo69, Mahajan90]. MaeB activity is highly regulated by key metabolites [Bologna07]. MaeB appears to be important for supplying NADPH during growth on two-carbon compounds [Wang11].

Initial purification studies working with E. coli K10 indicated that the enzyme was composed of 8 subunits [Spina70]. Further studies, with both E. coli W and K-12, have indicated 6 subunits [Iwakura79, Brown81] or again 8 subunits [Bologna07].

The C-terminal domain of MaeB is similar to phosphotransacetylases; it is not required for catalytic activity, but appears to be required for metabolic regulation and oligomerization [Bologna07].

Deletion of maeB abolishes NADP-dependent malic enzyme activity [vanderRest00]. maeB expression is upregulated in a pykF (pyruvate kinase) null mutant [Siddiquee04]. Overexpression of MaeB increases the production of C4 metabolites under anaerobic conditions with supplemental bicarbonate [Kwon07].

Locations: cytosol

Map Position: [2,574,120 <- 2,576,399] (55.48 centisomes)
Length: 2280 bp / 759 aa

Molecular Weight of Polypeptide: 82.417 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008111 , DIP:DIP-10141N , EchoBASE:EB3945 , EcoGene:EG14193 , EcoliWiki:b2463 , ModBase:P76558 , OU-Microarray:b2463 , PortEco:maeB , PR:PRO_000025146 , Pride:P76558 , Protein Model Portal:P76558 , RefSeq:NP_416958 , RegulonDB:G7293 , SMR:P76558 , String:511145.b2463 , UniProt:P76558

Relationship Links: InterPro:IN-FAMILY:IPR002505 , InterPro:IN-FAMILY:IPR012188 , InterPro:IN-FAMILY:IPR012301 , InterPro:IN-FAMILY:IPR012302 , InterPro:IN-FAMILY:IPR015884 , InterPro:IN-FAMILY:IPR016040 , Pfam:IN-FAMILY:PF00390 , Pfam:IN-FAMILY:PF01515 , Pfam:IN-FAMILY:PF03949 , Prosite:IN-FAMILY:PS00331 , Smart:IN-FAMILY:SM00919

In Paralogous Gene Group: 297 (4 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006108 - malate metabolic process Inferred by computational analysis [GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0004473 - malate dehydrogenase (decarboxylating) (NADP+) activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Bologna07, vanderRest00]
GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA01, Sanwal68]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0004471 - malate dehydrogenase (decarboxylating) (NAD+) activity Inferred by computational analysis [GOA01]
GO:0008948 - oxaloacetate decarboxylase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051287 - NAD binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [GOA01, Lasserre06]

MultiFun Terms: metabolism central intermediary metabolism

Essentiality data for maeB 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 ? 17-Nov-2011 by Keseler I , SRI International


Enzymatic reaction of: malate dehydrogenase

Synonyms: malic enzyme, malate dehydrogenase, NADP+-linked, pyruvic-malic carboxylase, (S)-malate:NADP+ oxidoreductase (oxaloacetate-decarboxylating)

EC Number: 1.1.1.40

(S)-malate + NADP+ <=> CO2 + pyruvate + NADPH

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 favored in the direction shown.

Alternative Substrates for (S)-malate [Comment 5 ]: oxaloacetate [Sanwal69 ]

In Pathways: gluconeogenesis I

Summary:
The kinetics of the reaction is sigmoidal; the Hill coefficient is 1.42 for K0.5,malate. Kinetic coefficients shown below are for the forward, decarboxylation reaction. The kcat, forward/kcat, reverse is 175.2 [Bologna07].

At pH 5, the enzyme can decarboxylate oxaloacetate, while at pH 7.5, oxaloacetate acts as an inhibitor. This oxaloacetate decarboxylase activity is inhibited by NADP+ [Sanwal69].

Cofactors or Prosthetic Groups: Mg2+ [Wang11, Bologna07], Mn2+ [Wang11, Sanwal68]

Alternative Cofactors for Mn2+: Mg2+

Activators (Unknown Mechanism): L-aspartate [Bologna07] , β-D-glucose 6-phosphate [Bologna07] , acetyl phosphate [Bologna07] , L-glutamate [Bologna07] , K+ [Sanwal69, Spina70, Bologna07, Brown81] , ammonium [Sanwal69, Spina70]

Inhibitors (Allosteric): NADH [Brown81, Sanwal69, Sanwal69a] , cyclic-AMP [Sanwal69, Sanwal69a] , acetyl-CoA [Sanwal68, Bologna07] , oxaloacetate [Sanwal69, Sanwal69a, Bologna07]

Inhibitors (Unknown Mechanism): NADP+ [Sanwal69, Sanwal69a, Brown81] , Zn2+ [Wang11] , fumarate [Bologna07]

Primary Physiological Regulators of Enzyme Activity: NADP+ , NADH , cyclic-AMP , acetyl-CoA

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
NADP+
41.5
[Bologna07]
(S)-malate
3410.0
66.6
[Bologna07, BRENDA14]

T(opt): 46 °C [BRENDA14, Wang11]

pH(opt): 7.8 [BRENDA14, Wang11], 7 [BRENDA14, Bologna07], 7.5 [Bologna07]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 1 -> 428
[UniProt10a]
UniProt: Malic enzyme; Sequence Annotation Type: region of interest;
Acetylation-Modification 56
[Zhang09, UniProt11a]
UniProt: N6-acetyllysine.
Nucleotide-Phosphate-Binding-Region 76 -> 83
[UniProt10a]
UniProt: NADP; Non-Experimental Qualifier: by similarity;
Active-Site 94
[UniProt10a]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 136
[UniProt10a]
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 137
[UniProt10a]
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 162
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 288
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Protein-Segment 429 -> 759
[UniProt10a]
UniProt: Phosphate acetyltransferase; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/26/2000 (pkarp) Merged genes G594/maeB and G7293/maeB
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Bologna07: Bologna FP, Andreo CS, Drincovich MF (2007). "Escherichia coli malic enzymes: two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure." J Bacteriol 189(16);5937-46. PMID: 17557829

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

Brown81: Brown DA, Cook RA (1981). "Role of metal cofactors in enzyme regulation. Differences in the regulatory properties of the Escherichia coli nicotinamide adenine dinucleotide phosphate specific malic enzyme, depending on whether magnesium ion or manganese ion serves as divalent cation." Biochemistry 1981;20(9);2503-12. PMID: 7016178

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

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Iwakura79: Iwakura M, Hattori J, Arita Y, Tokushige M, Katsuki H (1979). "Studies on regulatory functions of malic enzymes. VI. Purification and molecular properties of NADP-linked malic enzyme from Escherichia coli W." J Biochem (Tokyo) 1979;85(5);1355-65. PMID: 36376

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

Kwon07: Kwon YD, Kwon OH, Lee HS, Kim P (2007). "The effect of NADP-dependent malic enzyme expression and anaerobic C4 metabolism in Escherichia coli compared with other anaplerotic enzymes." J Appl Microbiol 103(6);2340-5. PMID: 18045419

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

Mahajan90: Mahajan SK, Chu CC, Willis DK, Templin A, Clark AJ (1990). "Physical analysis of spontaneous and mutagen-induced mutants of Escherichia coli K-12 expressing DNA exonuclease VIII activity." Genetics 1990;125(2);261-73. PMID: 2199308

Sanwal68: Sanwal BD, Wright JA, Smando R (1968). "Allosteric control of the activity of malic enzyme in Escherichia coli." Biochem Biophys Res Commun 31(4);623-7. PMID: 4385340

Sanwal69: Sanwal BD, Smando R (1969). "Malic enzyme of Escherichia coli. Diversity of the effectors controlling enzyme activity." J Biol Chem 1969;244(7);1817-23. PMID: 4388614

Sanwal69a: Sanwal BD, Smando R (1969). "Malic enzyme of Escherichia coli. Possible mechanism for allosteric effects." J Biol Chem 1969;244(7);1824-30. PMID: 4388615

Siddiquee04: Siddiquee KA, Arauzo-Bravo MJ, Shimizu K (2004). "Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli." FEMS Microbiol Lett 235(1);25-33. PMID: 15158258

Spina70: Spina J, Bright HJ, Rosenbloom J "Purification and Properties of L-Malic Enzyme from Escherichia coli." Biochemistry 1970;9(19):3794-3801.

Takeo69: Takeo K (1969). "Existence and properties of two malic enzymes in Escherichia coli especially of NAD-linked enzyme." J Biochem (Tokyo) 66(3);379-87. PMID: 4390688

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

vanderRest00: van der Rest ME, Frank C, Molenaar D (2000). "Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli." J Bacteriol 2000;182(24);6892-9. PMID: 11092847

Wang11: Wang B, Wang P, Zheng E, Chen X, Zhao H, Song P, Su R, Li X, Zhu G (2011). "Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli." J Microbiol 49(5);797-802. PMID: 22068497

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


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 Wed Nov 26, 2014, biocyc11.