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Literature summary extracted from

  • Hsieh, J.; Li, S.; Chen, M.; Yang, P.; Chen, H.; Chan, N.; Liu, J.; Hung, H.
    Structural characteristics of the nonallosteric human cytosolic malic enzyme (2014), Biochim. Biophys. Acta, 1844, 1773-1783.
    View publication on PubMed

Activating Compound

EC Number Activating Compound Comment Organism Structure
1.1.1.38 fumarate mitochondrial NAD(P)+-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by fumarate Homo sapiens
1.1.1.38 additional information cytosolic NADP+-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme Homo sapiens
1.1.1.40 additional information cannot be activated by fumarate Homo sapiens
1.1.1.40 additional information no activation by fumarate Homo sapiens

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.38 recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3) Homo sapiens
1.1.1.40 expressed in Escherichia coli BL21(DE3) cells Homo sapiens
1.1.1.40 recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and ultrafiltration Homo sapiens

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.40 hanging drop vapor diffusion method, using 250 mM LiCl and 19% (w/v) PEG 3350 Homo sapiens
1.1.1.40 purified apoenzyme, hanging drop vapor diffusion method, 6 mg/ml protein is crystallized against a reservoir solution containing 250 mM LiCl and 19% w/v PEG 3350, room temperature, 5-7 days, X-ray diffraction structure determination and analysis at 2.55 A resolution, molecular replacement using the structure of pigeon c-NADP-ME in complex with NADP+, Mn2+, and oxalate as search model, modelling Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
1.1.1.38 K57S/E59N/K73E/D102S site-directed mutagenesis Homo sapiens
1.1.1.40 E73K site-directed mutagenesis Homo sapiens
1.1.1.40 E73K the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 K57S/E59N/K73E/D102S site-directed mutagenesis, the mutant is primarily monomeric with some dimer formation Homo sapiens
1.1.1.40 additional information multiple residues corresponding to the fumarate-binding site are mutated in human c-NADP-ME to correspond to those found in human m-NAD(P)-ME, EC 1.1.1.39. No significant difference between the wild-type and mutant enzymes in Km values for NADP+ and malate, and in kcat values. A chimeric enzyme, [51-105]_c-NADP-ME, is designed to include the putative fumarate-binding site ofm-NAD(P)-ME at the dimer interface of c-NADP-ME, but the chimera remains nonallosteric Homo sapiens
1.1.1.40 N59E site-directed mutagenesis Homo sapiens
1.1.1.40 N59E the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 N59E/E73K site-directed mutagenesis Homo sapiens
1.1.1.40 N59E/E73K the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 N59E/E73K/S102D site-directed mutagenesis Homo sapiens
1.1.1.40 N59E/E73K/S102D the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 S102D site-directed mutagenesis Homo sapiens
1.1.1.40 S102D the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 S57K site-directed mutagenesis Homo sapiens
1.1.1.40 S57K the mutant shows increased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 S57K/N59E/E73K site-directed mutagenesis Homo sapiens
1.1.1.40 S57K/N59E/E73K the mutant shows wild type turnover numbers for (S)-malate and NADP+ Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D the mutant shows increased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D site-directed mutagenesis, the mutant is tetrameric Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G site-directed mutagenesis, the mutant is tetrameric Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H site-directed mutagenesis Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H site-directed mutagenesis Homo sapiens
1.1.1.40 S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.38 additional information
-
 additional information cytosolic NADP+-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme Homo sapiens
1.1.1.38 0.3
-
 NADH pH 7.4, 30°C, recombinant mutant K57S/E59N/K73E/D102S Homo sapiens
1.1.1.38 0.3
-
 NADH pH 7.4, 30°C, recombinant mutant K57S/E59N/K73E/D102S with 5 mM fumarate Homo sapiens
1.1.1.38 0.3
-
 NADH pH 7.4, 30°C, recombinant wild-type with 5 mM fumarate Homo sapiens
1.1.1.38 1.4
-
 NADH pH 7.4, 30°C, recombinant wild-type Homo sapiens
1.1.1.38 3
-
 (S)-malate pH 7.4, 30°C, recombinant mutant K57S/E59N/K73E/D102S Homo sapiens
1.1.1.38 3.6
-
 (S)-malate pH 7.4, 30°C, recombinant mutant K57S/E59N/K73E/D102S with 5 mM fumarate Homo sapiens
1.1.1.38 4.6
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme with 5 mM fumarate Homo sapiens
1.1.1.38 15.6
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
1.1.1.40 0.0018
-
 NADP+ mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0018
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H Homo sapiens
1.1.1.40 0.0019
-
 NADP+ wild type enzyme, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0019
-
 NADP+ mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0019
-
 NADPH pH 7.4, 30°C, recombinant mutant 57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G Homo sapiens
1.1.1.40 0.0019
-
 NADPH pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
1.1.1.40 0.0023
-
 NADP+ mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0023
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H Homo sapiens
1.1.1.40 0.0027
-
 NADPH pH 7.4, 30°C, recombinant mutant [51-105]_c-NADP-ME Homo sapiens
1.1.1.40 0.0031
-
 NADP+ mutant enzyme S57K/N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0031
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D Homo sapiens
1.1.1.40 0.0045
-
 NADP+ mutant enzyme N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0045
-
 NADP+ mutant enzyme S57K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0045
-
 NADPH pH 7.4, 30°C, recombinant mutant N59E/E73K/S102D Homo sapiens
1.1.1.40 0.0045
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K Homo sapiens
1.1.1.40 0.0046
-
 NADP+ mutant enzyme N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0046
-
 NADPH pH 7.4, 30°C, recombinant mutant N59E/E73K Homo sapiens
1.1.1.40 0.0049
-
 NADP+ mutant enzyme S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0049
-
 NADPH pH 7.4, 30°C, recombinant mutant S102D Homo sapiens
1.1.1.40 0.0069
-
 NADP+ mutant enzyme S57K/N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0069
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K Homo sapiens
1.1.1.40 0.0089
-
 NADP+ mutant enzyme N59E, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0089
-
 NADPH pH 7.4, 30°C, recombinant mutant N59E Homo sapiens
1.1.1.40 0.0125
-
 NADP+ mutant enzyme E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.0125
-
 NADPH pH 7.4, 30°C, recombinant mutant E73K Homo sapiens
1.1.1.40 0.8
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.8
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.8
-
 (S)-malate pH 7.4, 30°C, recombinant mutant 57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G Homo sapiens
1.1.1.40 0.8
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H Homo sapiens
1.1.1.40 0.8
-
 (S)-malate pH 7.4, 30°C, recombinant mutant [51-105]_c-NADP-ME Homo sapiens
1.1.1.40 0.9
-
 (S)-malate mutant enzyme N59E, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 0.9
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E Homo sapiens
1.1.1.40 1
-
 (S)-malate mutant enzyme S57K/N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K Homo sapiens
1.1.1.40 1
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H Homo sapiens
1.1.1.40 1.2
-
 (S)-malate wild type enzyme, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.2
-
 (S)-malate mutant enzyme N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.2
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.2
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K Homo sapiens
1.1.1.40 1.2
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
1.1.1.40 1.3
-
 (S)-malate mutant enzyme E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.3
-
 (S)-malate pH 7.4, 30°C, recombinant mutant E73K Homo sapiens
1.1.1.40 1.3
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D Homo sapiens
1.1.1.40 1.4
-
 (S)-malate mutant enzyme N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.4
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K/S102D Homo sapiens
1.1.1.40 1.6
-
 (S)-malate mutant enzyme S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.6
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S102D Homo sapiens
1.1.1.40 1.7
-
 (S)-malate mutant enzyme S57K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 1.7
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K Homo sapiens

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.1.1.38 cytosol
-
 Homo sapiens 5829
-
1.1.1.40 cytosol
-
 Homo sapiens 5829
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.40 Mg2+ activates Homo sapiens
1.1.1.40 Mg2+ dependent on Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.38 (S)-malate + NAD+ Homo sapiens
-
 pyruvate + CO2 + NADH
-
 r
1.1.1.40 (S)-malate + NADP+ Homo sapiens
-
 pyruvate + CO2 + NADPH
-
 r
1.1.1.40 (S)-malate + NADP+ Homo sapiens
-
 pyruvate + CO2 + NADPH + H+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.38 Homo sapiens P23368
-
-
1.1.1.40 Homo sapiens P48163
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.38 recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and ultrafiltration Homo sapiens
1.1.1.40 Ni-NTA column chromatography Homo sapiens

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.38 (S)-malate + NAD+
-
 Homo sapiens pyruvate + CO2 + NADH
-
 r
1.1.1.40 (S)-malate + NADP+
-
 Homo sapiens pyruvate + CO2 + NADPH
-
 r
1.1.1.40 (S)-malate + NADP+
-
 Homo sapiens pyruvate + CO2 + NADPH + H+
-
 ?

Subunits

EC Number Subunits Comment Organism
1.1.1.38 dimer and tetramer
-
 Homo sapiens
1.1.1.40 homotetramer x-ray crystallography Homo sapiens
1.1.1.40 More structure comparisons, overview Homo sapiens
1.1.1.40 tetramer a dimer of dimers. The c-NADP-ME monomer is composed of four domains. Domain A (residues 23-130) is predominantly helical and confers the ability to bind fumarate. Domain B (residues 131-277 and 464-535) contains a central five-stranded parallel beta-sheet surrounded by helices on both sides. Domain C (residues 278-463) exhibits a dinucleotide-binding Rossmann fold with a modification: strand beta3 is replaced by a short antiparallel beta-strand. Domain D (residues 536-579) contains one helix followed by a long extended random coil structure protruding away from the ordered portion of the ME monomer. The active site of ME is located at the interface of domains B and C, whereas residues in domains A and D primarily participate in the formation of dimers and tetramers Homo sapiens

Synonyms

EC Number Synonyms Comment Organism
1.1.1.38 m-NAD(P)-ME
-
 Homo sapiens
1.1.1.38 mitochondrial NAD(P)+-dependent malic enzyme
-
 Homo sapiens
1.1.1.40 c-NADP-ME
-
 Homo sapiens
1.1.1.40 cytosolic NADP+-dependent malic enzyme
-
 Homo sapiens

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.1.1.38 30
-
 assay at Homo sapiens
1.1.1.40 30
-
 assay at Homo sapiens

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.38 5
-
 (S)-malate pH 7.4, 30°C, recombinant mutant K57S/E59N/K73E/D102S with or without 5 mM fumarate Homo sapiens
1.1.1.38 43
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
1.1.1.38 55
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme with 5 mM fumarate Homo sapiens
1.1.1.40 2 8 (S)-malate mutant enzyme N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 2 8 (S)-malate mutant enzyme N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 2 8 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K Homo sapiens
1.1.1.40 2 8 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K/S102D Homo sapiens
1.1.1.40 3 6 (S)-malate pH 7.4, 30°C, recombinant mutant [51-105]_c-NADP-ME Homo sapiens
1.1.1.40 21
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 21
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H Homo sapiens
1.1.1.40 22
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 22
-
 (S)-malate pH 7.4, 30°C, recombinant mutant 57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G Homo sapiens
1.1.1.40 23
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 23
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H Homo sapiens
1.1.1.40 27
-
 (S)-malate mutant enzyme N59E, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 27
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E Homo sapiens
1.1.1.40 29
-
 (S)-malate mutant enzyme S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 29
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S102D Homo sapiens
1.1.1.40 30
-
 (S)-malate wild type enzyme, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 30
-
 (S)-malate mutant enzyme E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 30
-
 (S)-malate mutant enzyme S57K/N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 30
-
 (S)-malate pH 7.4, 30°C, recombinant mutant E73K Homo sapiens
1.1.1.40 30
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K Homo sapiens
1.1.1.40 30
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
1.1.1.40 31
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 31
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D Homo sapiens
1.1.1.40 32
-
 (S)-malate mutant enzyme S57K, at pH 7.4 and 30°C Homo sapiens
1.1.1.40 32
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K Homo sapiens

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.38 7.4
-
 assay at Homo sapiens
1.1.1.40 7.4
-
 assay at Homo sapiens

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.38 additional information the isoenzyme can also use NADP+ but is more effective with NAD+ Homo sapiens
1.1.1.38 NAD+
-
 Homo sapiens
1.1.1.38 NADH
-
 Homo sapiens
1.1.1.38 NADP+
-
 Homo sapiens
1.1.1.38 NADPH
-
 Homo sapiens
1.1.1.40 NADP+
-
 Homo sapiens
1.1.1.40 NADPH
-
 Homo sapiens

General Information

EC Number General Information Comment Organism
1.1.1.38 additional information the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME, EC 1.1.1.38 and c-NADP-ME, EC 1.1.1.40. The structural features near the fumarate binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME. Lys57 plays functional roles in both the allosteric regulation and the subunit-subunit interaction of humanm-NAD(P)-ME Homo sapiens
1.1.1.40 additional information the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME, EC 1.1.1.39 and c-NADP-ME, EC 1.1.1.40. The structural features near the fumarate binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME Homo sapiens