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Literature summary for 1.1.1.40 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
Search for more literature for 1.1.1.40

Activating Compound

Activating Compound Comment Organism Structure
additional information cannot be activated by fumarate Homo sapiens
additional information no activation by fumarate Homo sapiens

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment) Organism
hanging drop vapor diffusion method, using 250 mM LiCl and 19% (w/v) PEG 3350 Homo sapiens
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

Protein Variants Comment Organism
E73K site-directed mutagenesis Homo sapiens
E73K the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
K57S/E59N/K73E/D102S site-directed mutagenesis, the mutant is primarily monomeric with some dimer formation Homo sapiens
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
N59E site-directed mutagenesis Homo sapiens
N59E the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
N59E/E73K site-directed mutagenesis Homo sapiens
N59E/E73K the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
N59E/E73K/S102D site-directed mutagenesis Homo sapiens
N59E/E73K/S102D the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
S102D site-directed mutagenesis Homo sapiens
S102D the mutant shows decreased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
S57K site-directed mutagenesis Homo sapiens
S57K the mutant shows increased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
S57K/N59E/E73K site-directed mutagenesis Homo sapiens
S57K/N59E/E73K the mutant shows wild type turnover numbers for (S)-malate and NADP+ Homo sapiens
S57K/N59E/E73K/S102D the mutant shows increased turnover numbers for (S)-malate and NADP+ compared to the wild type enzyme Homo sapiens
S57K/N59E/E73K/S102D site-directed mutagenesis, the mutant is tetrameric Homo sapiens
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
S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G site-directed mutagenesis, the mutant is tetrameric Homo sapiens
S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H site-directed mutagenesis Homo sapiens
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
S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H site-directed mutagenesis Homo sapiens
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]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
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
0.0018
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H Homo sapiens
0.0019
-
 NADP+ wild type enzyme, at pH 7.4 and 30°C Homo sapiens
0.0019
-
 NADP+ mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G, at pH 7.4 and 30°C Homo sapiens
0.0019
-
 NADPH pH 7.4, 30°C, recombinant mutant 57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G Homo sapiens
0.0019
-
 NADPH pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
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
0.0023
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H Homo sapiens
0.0027
-
 NADPH pH 7.4, 30°C, recombinant mutant [51-105]_c-NADP-ME Homo sapiens
0.0031
-
 NADP+ mutant enzyme S57K/N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
0.0031
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D Homo sapiens
0.0045
-
 NADP+ mutant enzyme N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
0.0045
-
 NADP+ mutant enzyme S57K, at pH 7.4 and 30°C Homo sapiens
0.0045
-
 NADPH pH 7.4, 30°C, recombinant mutant N59E/E73K/S102D Homo sapiens
0.0045
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K Homo sapiens
0.0046
-
 NADP+ mutant enzyme N59E/E73K, at pH 7.4 and 30°C Homo sapiens
0.0046
-
 NADPH pH 7.4, 30°C, recombinant mutant N59E/E73K Homo sapiens
0.0049
-
 NADP+ mutant enzyme S102D, at pH 7.4 and 30°C Homo sapiens
0.0049
-
 NADPH pH 7.4, 30°C, recombinant mutant S102D Homo sapiens
0.0069
-
 NADP+ mutant enzyme S57K/N59E/E73K, at pH 7.4 and 30°C Homo sapiens
0.0069
-
 NADPH pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K Homo sapiens
0.0089
-
 NADP+ mutant enzyme N59E, at pH 7.4 and 30°C Homo sapiens
0.0089
-
 NADPH pH 7.4, 30°C, recombinant mutant N59E Homo sapiens
0.0125
-
 NADP+ mutant enzyme E73K, at pH 7.4 and 30°C Homo sapiens
0.0125
-
 NADPH pH 7.4, 30°C, recombinant mutant E73K Homo sapiens
0.8
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G, at pH 7.4 and 30°C Homo sapiens
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
0.8
-
 (S)-malate pH 7.4, 30°C, recombinant mutant 57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G Homo sapiens
0.8
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H Homo sapiens
0.8
-
 (S)-malate pH 7.4, 30°C, recombinant mutant [51-105]_c-NADP-ME Homo sapiens
0.9
-
 (S)-malate mutant enzyme N59E, at pH 7.4 and 30°C Homo sapiens
0.9
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E Homo sapiens
1
-
 (S)-malate mutant enzyme S57K/N59E/E73K, at pH 7.4 and 30°C Homo sapiens
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
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K Homo sapiens
1
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H Homo sapiens
1.2
-
 (S)-malate wild type enzyme, at pH 7.4 and 30°C Homo sapiens
1.2
-
 (S)-malate mutant enzyme N59E/E73K, at pH 7.4 and 30°C Homo sapiens
1.2
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.2
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K Homo sapiens
1.2
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
1.3
-
 (S)-malate mutant enzyme E73K, at pH 7.4 and 30°C Homo sapiens
1.3
-
 (S)-malate pH 7.4, 30°C, recombinant mutant E73K Homo sapiens
1.3
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D Homo sapiens
1.4
-
 (S)-malate mutant enzyme N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
1.4
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K/S102D Homo sapiens
1.6
-
 (S)-malate mutant enzyme S102D, at pH 7.4 and 30°C Homo sapiens
1.6
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S102D Homo sapiens
1.7
-
 (S)-malate mutant enzyme S57K, at pH 7.4 and 30°C Homo sapiens
1.7
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K Homo sapiens

Localization

Localization Comment Organism GeneOntology No. Textmining
cytosol
-
 Homo sapiens 5829
-

Metals/Ions

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

Natural Substrates/ Products (Substrates)

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

Organism

Organism UniProt Comment Textmining
Homo sapiens P48163
-
-

Purification (Commentary)

Purification (Comment) Organism
Ni-NTA column chromatography Homo sapiens

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(S)-malate + NADP+
-
 Homo sapiens pyruvate + CO2 + NADPH
-
 r
(S)-malate + NADP+
-
 Homo sapiens pyruvate + CO2 + NADPH + H+
-
 ?

Subunits

Subunits Comment Organism
homotetramer x-ray crystallography Homo sapiens
More structure comparisons, overview Homo sapiens
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

Synonyms Comment Organism
c-NADP-ME
-
 Homo sapiens
cytosolic NADP+-dependent malic enzyme
-
 Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
 assay at Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2 8 (S)-malate mutant enzyme N59E/E73K, at pH 7.4 and 30°C Homo sapiens
2 8 (S)-malate mutant enzyme N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
2 8 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K Homo sapiens
2 8 (S)-malate pH 7.4, 30°C, recombinant mutant N59E/E73K/S102D Homo sapiens
3 6 (S)-malate pH 7.4, 30°C, recombinant mutant [51-105]_c-NADP-ME Homo sapiens
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
21
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/D90E/K106S/Q121S/L125H Homo sapiens
22
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G, at pH 7.4 and 30°C Homo sapiens
22
-
 (S)-malate pH 7.4, 30°C, recombinant mutant 57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G Homo sapiens
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
23
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G/K106S/Q121S/L125H Homo sapiens
27
-
 (S)-malate mutant enzyme N59E, at pH 7.4 and 30°C Homo sapiens
27
-
 (S)-malate pH 7.4, 30°C, recombinant mutant N59E Homo sapiens
29
-
 (S)-malate mutant enzyme S102D, at pH 7.4 and 30°C Homo sapiens
29
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S102D Homo sapiens
30
-
 (S)-malate wild type enzyme, at pH 7.4 and 30°C Homo sapiens
30
-
 (S)-malate mutant enzyme E73K, at pH 7.4 and 30°C Homo sapiens
30
-
 (S)-malate mutant enzyme S57K/N59E/E73K, at pH 7.4 and 30°C Homo sapiens
30
-
 (S)-malate pH 7.4, 30°C, recombinant mutant E73K Homo sapiens
30
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K Homo sapiens
30
-
 (S)-malate pH 7.4, 30°C, recombinant wild-type enzyme Homo sapiens
31
-
 (S)-malate mutant enzyme S57K/N59E/E73K/S102D, at pH 7.4 and 30°C Homo sapiens
31
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K/N59E/E73K/S102D Homo sapiens
32
-
 (S)-malate mutant enzyme S57K, at pH 7.4 and 30°C Homo sapiens
32
-
 (S)-malate pH 7.4, 30°C, recombinant mutant S57K Homo sapiens

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
 assay at Homo sapiens

Cofactor

Cofactor Comment Organism Structure
NADP+
-
 Homo sapiens
NADPH
-
 Homo sapiens

General Information

General Information Comment Organism
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