1.1.1.85: 3-isopropylmalate dehydrogenase

This is an abbreviated version, for detailed information about 3-isopropylmalate dehydrogenase, go to the full flat file.

Reaction

(2R,3S)-3-isopropylmalate
+
NAD+
=
(2S)-2-isopropyl-3-oxosuccinate
+
NADH
+
H+

Synonyms

2-hydroxy-4-methyl-3-carboxyvalerate:NAD+ oxidoreductase, 2R,3S-isopropylmalate:NAD+ oxidoreductase (decaboxylating), 3-IPM dehydrogenase, 3-IPM-DH, 3-isopropylmalate dehydrogenase, 3-isopropylmalateDH, APS IPMDH, beta-IPM dehydrogenase, beta-IPMDH, beta-isopropylmalate dehydrogenase, beta-isopropylmalic enzyme, Bs3-isopropylmalateDH, dehydrogenase, 3-isopropylmalate, IMDH, IPMDH, IPMDH1, IPMDH2, IPMDH3, isopropylmalate dehydrogenase, leuB, NAD-dependent isopropylmalate dehydrogenase, Saci_0600, SbIPMDH, SoIPMDH, threo-Ds-3-isopropylmalate dehydrogenase, Tt-beta-3-isopropylmalateDH, two-domain 3-isopropylmalate dehydrogenase, Ydr417cp

ECTree

     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.85 3-isopropylmalate dehydrogenase

Crystallization

Crystallization on EC 1.1.1.85 - 3-isopropylmalate dehydrogenase

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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme in complex with 3-isopropylmalate
-
in complex with either isopropylmalate and Mg2+ or NAD+, hanging drop vapor diffusion method, using 1.0 M ammonium phosphate, 0.1 M imidazole, pH 8.0
to 2.25 A resolution. Modeling of 3-isopropylmalate binding in the isoform IPMDH2 active site. Results suggest that substitution of one active site residue may lead to altered substrate specificity and metabolic function
hanging drop vapor diffusion method, chimeric enzyme constructed by fusing the gene of Bacillus subtilis and Thermus thermophilus coding for 3-isopropylmalate dehydrogenase, expression in Escherichia coli
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crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus
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The crystal structure is determined at 1.65 A resolution. The crystals contain two functional dimers in the asymmetric unit in an arrangement close to a tetramer of D2 symmetry.
crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus
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to 1.5 A resolution. Comparison of enzyme structures from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1. The Shewanella benthica enzyme is in a more open form and has a larger internal cavity volume than Shewanella oneidensis IPMDH at atmospheric pressure. The loosely packed structure of Shewanella benthica IPMDH may help it to avoid pressure-induced distortion of the native structure and to remain active at higher pressures than Shewanella oneidensis IPMDH
-
structures of 3-isopropylmalate dehydrogenase at about 2 A resolution under pressures ranging from 0.1 to 650 MPa. Most of the protein cavities are monotonically compressed as the pressure increases. The volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity occurs at pressures over 410 MPa.The generation of a new cleft on the molecular surface accompanied by water penetration can be observed at pressures over 580 MPa
-
to 1.5 A resolution. Comparison of enzyme structures from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1. The Shewanella benthica enzyme is in a more open form and has a larger internal cavity volume than Shewanella oneidensis IPMDH at atmospheric pressure. The loosely packed structure of Shewanella benthica IPMDH may help it to avoid pressure-induced distortion of the native structure and to remain active at higher pressures than Shewanella oneidensis IPMDH
-
in complex with (2R,3S)-3-isopropylmalate and Mg2+, hanging drop vapor diffusion method, using 2.0 M (NH4)2SO4, 200 mM NaCl, and 100 mM sodium cacodylate pH 6.5
crystallized by the vapor-diffusion method, space group P2221. The crystallization requires 2-methyl-2,4-pentanediol to avoid twinning of the crystals
-
ammonium sulfate precipitation, crystals diffract beyond 2.5 A resolution and are quite stable against X-rays, recombinant enzyme expressed in Escherichia coli
-
apo-form without substrate and in complex with the divalent metal–ion, in complexes with both Mn2+ and 3-isopropylmalate, as well as with both Mn2+ and NADH, at resolutions ranging from 1.8 to 2.5 A. Identification of two hinges at the interdomain region, hinge 1 between alphad and betaF as well as hinge 2 between alphah and betaE with a possible operational mechanism upon the action of the substrates. The interactions of the protein with Mn2+ and isopropylmalate are mainly responsible for the domain closure. Upon binding into the cleft of the interdomain region, the substrate isopropylmalate induces a relative movement of the secondary structural elements betaE, betaF, betaG, alphad and alphah. A movement of the loop bearing the amino acid Tyr139 precedes the interacting arm of the subunit. The tyrosyl ring rotates and moves by at least 5 A upon substrate binding. Thereby, new hydrophobic interactions are formed above the buried isopropyl-group of isopropylmalate. Domain closure is then completed only through subunit interactions. A loop of one subunit that is inserted into the interdomain cavity of the other subunit extends the area with the hydrophobic interactions, providing an example of the cooperativity between interdomain and intersubunit interactions
-
crystal structure of mutant H15Y/E57V/S72I/R85M/Y86A/M208T/F217Y/V238M/R310M is determined at 2.4 A
crystal structure of Thermus thermophilus IPMDH in a ternary complex with NAD+ and the inhibitor ((2S,3S)-3-methylmercaptomalate) is determined at 2.8 A resolution. The inhibitor exists as a decarboxylated product with an enol/enolate form in the active site. The product interacts with Arg94, Asn102, Ser259, Glu270, and a water molecule hydrogen-bonding with Arg132. All interactions between the product and the enzyme are observed in the position associated with keto-enol tautomerization
-
enzyme in complex with NAD+
-
hanging drop vapor diffusion method, chimeric enzyme constructed by fusing the gene of Bacillus subtilis and Thermus thermophilus coding for 3-isopropylmalate dehydrogenase, expression in Escherichia coli
-
in complex with Mn2+, (2R,3S)-3-isopropylmalate, and NADH, hanging drop vapor diffusion method, using 20% (w/v) PEG 6000, 0.1 M MOPS/KOH, pH 7.6, and 10% (v/v) ethanol
-
mutant enzyme E270A, hanging drop vapor diffusion method, using 20% (w/v) PEG 6000, 0.1 M MOPS/KOH pH 7.6, and 10% (v/v) ethanol
-
mutant enzymes A172V, A172G and A172F. As in the case of A172L enzyme, the A172F mutant can not be crystallized by the salting-out technique with ammonium sulfate. The crystal is obtained at pH 4.8 using polyethylene glycol 4000 as a precipitant. Crystals of mutant enzyme A172E are obtained from a drop equilibrated with reservoir solution consisting of 0.8 M ammonium sulfate pH 6.0 at either 15°C or 20°C K. Two types of crystals: one hexagonal bipyramidal and the other is tetragonal
-
recombinant enzyme expressed in Escherichia coli, ammonium sulfate precipitation
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study of the mutant enzymes G240A and L246E/V249M by X-ray crystallography
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using the hanging-drop vapour diffusion method crystals of Tt-IPMDH are grown in the following combinations: Apo Tt-IPMDH (crystal diffracted to a resolution of about 1.8 A), Tt-IPMDH in complex with Mn2+ (crystal diffracted to a resolution of about 2.5 A), Tt-IPMDH in complex with Mn2+ and beta-3-isopropylmalate (crystal diffracted to a resolution of 2.2 A), Tt-IPMDH in complex with Mn2+ and NADH (crystal diffracted to a resolution of 2.5 A), and Tt-IPMDH in complex with Mn2+, beta-3-isopropylmalate and NADH (crystal diffracted to a resolution of 2.75 A)
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