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Miggiano R, Martignon S, Minassi A, Rossi F, Rizzi M. Crystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase (LeuB) in complex with the inhibitor O-isobutenyl oxalylhydroxamate. Biochem Biophys Res Commun 2020; 524:996-1002. [DOI: 10.1016/j.bbrc.2020.02.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 11/25/2022]
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2
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Lee SG, Nwumeh R, Jez JM. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS. J Biol Chem 2016; 291:13421-30. [PMID: 27137927 DOI: 10.1074/jbc.m116.730358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Isopropylmalate dehydrogenase (IPMDH) and 3-(2'-methylthio)ethylmalate dehydrogenase catalyze the oxidative decarboxylation of different β-hydroxyacids in the leucine- and methionine-derived glucosinolate biosynthesis pathways, respectively, in plants. Evolution of the glucosinolate biosynthetic enzyme from IPMDH results from a single amino acid substitution that alters substrate specificity. Here, we present the x-ray crystal structures of Arabidopsis thaliana IPMDH2 (AtIPMDH2) in complex with either isopropylmalate and Mg(2+) or NAD(+) These structures reveal conformational changes that occur upon ligand binding and provide insight on the active site of the enzyme. The x-ray structures and kinetic analysis of site-directed mutants are consistent with a chemical mechanism in which Lys-232 activates a water molecule for catalysis. Structural analysis of the AtIPMDH2 K232M mutant and isothermal titration calorimetry supports a key role of Lys-232 in the reaction mechanism. This study suggests that IPMDH-like enzymes in both leucine and glucosinolate biosynthesis pathways use a common mechanism and that members of the β-hydroxyacid reductive decarboxylase family employ different active site features for similar reactions.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Ronald Nwumeh
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
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3
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Palló A, Oláh J, Gráczer E, Merli A, Závodszky P, Weiss MS, Vas M. Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. FEBS J 2014; 281:5063-76. [PMID: 25211160 DOI: 10.1111/febs.13044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn(2+) , its substrate isopropylmalate and its co-factor product NADH at 2.0 Å resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 Å. The structure further shows binding of a K(+) ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD(+) is easily possible, with an activation energy of approximately 15 kcal·mol(-1) . The activation energy increases by approximately 4-6 kcal·mol(-1) when the K(+) ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the ε-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule. DATABASE Structural data have been submitted to the Protein Data Bank under accession number 4F7I.
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Affiliation(s)
- Anna Palló
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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4
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Coenzyme Activity of NAD Analogs for 3-Isopropylmalate Dehydrogenase fromThermus thermophilusHB8. Biosci Biotechnol Biochem 2014; 63:1647-9. [DOI: 10.1271/bbb.63.1647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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5
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Gráczer É, Lionne C, Závodszky P, Chaloin L, Vas M. Transient kinetic studies reveal isomerization steps along the kinetic pathway ofThermus thermophilus3-isopropylmalate dehydrogenase. FEBS J 2013; 280:1764-72. [DOI: 10.1111/febs.12191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Éva Gráczer
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest; Hungary
| | - Corinne Lionne
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS); UMR 5236 CNRS; University Montpellier I, University Montpellier II; France
| | - Péter Závodszky
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest; Hungary
| | - Laurent Chaloin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS); UMR 5236 CNRS; University Montpellier I, University Montpellier II; France
| | - Mária Vas
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest; Hungary
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6
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Nagae T, Kato C, Watanabe N. Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:265-8. [PMID: 22442218 PMCID: PMC3310526 DOI: 10.1107/s1744309112001443] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 01/12/2012] [Indexed: 11/10/2022]
Abstract
Organisms living in deep seas such as the Mariana Trench must be adapted to the extremely high pressure environment. For example, the 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 (SbIPMDH) remains active in extreme conditions under which that from the land bacterium S. oneidensis MR-1 (SoIPMDH) becomes inactivated. In order to unravel the differences between these two IPMDHs, their structures were determined at ~1.5 Å resolution. Comparison of the structures of the two enzymes shows that SbIPMDH is in a more open form and has a larger internal cavity volume than SoIPMDH at atmospheric pressure. This loosely packed structure of SbIPMDH could help it to avoid pressure-induced distortion of the native structure and to remain active at higher pressures than SoIPMDH.
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Affiliation(s)
- Takayuki Nagae
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Japan
| | - Chiaki Kato
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Japan
- Synchrotron Radiation Research Center, Nagoya University, Japan
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7
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Bulfer SL, Hendershot JM, Trievel RC. Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe. Proteins 2012; 80:661-6. [PMID: 22105743 PMCID: PMC4332711 DOI: 10.1002/prot.23231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 10/17/2011] [Indexed: 11/09/2022]
Abstract
Homoisocitrate dehydrogenase (HICDH) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the α-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. This enzyme represents a potential target for anti-fungal drug design. Here, we describe the first crystal structures of a fungal HICDH, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. The structures illustrate the homology of HICDH with other β-hydroxyacid oxidative decarboxylases and reveal key differences with the active site of Thermus thermophilus HICDH that provide insights into the differences in substrate specificity of these enzymes.
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Affiliation(s)
- Stacie L Bulfer
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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8
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Gráczer É, Konarev PV, Szimler T, Bacsó A, Bodonyi A, Svergun DI, Závodszky P, Vas M. Essential role of the metal-ion in the IPM-assisted domain closure of 3-isopropylmalate dehydrogenase. FEBS Lett 2011; 585:3297-302. [DOI: 10.1016/j.febslet.2011.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 09/06/2011] [Accepted: 09/08/2011] [Indexed: 11/27/2022]
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9
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Sidhu NS, Delbaere LTJ, Sheldrick GM. Structure of a highly NADP+-specific isocitrate dehydrogenase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:856-69. [PMID: 21931217 DOI: 10.1107/s0907444911028575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/16/2011] [Indexed: 11/10/2022]
Abstract
Isocitrate dehydrogenase catalyzes the first oxidative and decarboxylation steps in the citric acid cycle. It also lies at a crucial bifurcation point between CO2-generating steps in the cycle and carbon-conserving steps in the glyoxylate bypass. Hence, the enzyme is a focus of regulation. The bacterial enzyme is typically dependent on the coenzyme nicotinamide adenine dinucleotide phosphate. The monomeric enzyme from Corynebacterium glutamicum is highly specific towards this coenzyme and the substrate isocitrate while retaining a high overall efficiency. Here, a 1.9 Å resolution crystal structure of the enzyme in complex with its coenzyme and the cofactor Mg2+ is reported. Coenzyme specificity is mediated by interactions with the negatively charged 2'-phosphate group, which is surrounded by the side chains of two arginines, one histidine and, via a water, one lysine residue, forming ion pairs and hydrogen bonds. Comparison with a previous apoenzyme structure indicates that the binding site is essentially preconfigured for coenzyme binding. In a second enzyme molecule in the asymmetric unit negatively charged aspartate and glutamate residues from a symmetry-related enzyme molecule interact with the positively charged arginines, abolishing coenzyme binding. The holoenzyme from C. glutamicum displays a 36° interdomain hinge-opening movement relative to the only previous holoenzyme structure of the monomeric enzyme: that from Azotobacter vinelandii. As a result, the active site is not blocked by the bound coenzyme as in the closed conformation of the latter, but is accessible to the substrate isocitrate. However, the substrate-binding site is disrupted in the open conformation. Hinge points could be pinpointed for the two molecules in the same crystal, which show a 13° hinge-bending movement relative to each other. One of the two pairs of hinge residues is intimately flanked on both sides by the isocitrate-binding site. This suggests that binding of a relatively small substrate (or its competitive inhibitors) in tight proximity to a hinge point could lead to large conformational changes leading to a closed, presumably catalytically active (or inactive), conformation. It is possible that the small-molecule concerted inhibitors glyoxylate and oxaloacetate similarly bind close to the hinge, leading to an inactive conformation of the enzyme.
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Affiliation(s)
- Navdeep S Sidhu
- Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
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10
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He Y, Galant A, Pang Q, Strul JM, Balogun SF, Jez JM, Chen S. Structural and functional evolution of isopropylmalate dehydrogenases in the leucine and glucosinolate pathways of Arabidopsis thaliana. J Biol Chem 2011; 286:28794-28801. [PMID: 21697089 DOI: 10.1074/jbc.m111.262519] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The methionine chain-elongation pathway is required for aliphatic glucosinolate biosynthesis in plants and evolved from leucine biosynthesis. In Arabidopsis thaliana, three 3-isopropylmalate dehydrogenases (AtIPMDHs) play key roles in methionine chain-elongation for the synthesis of aliphatic glucosinolates (e.g. AtIPMDH1) and leucine (e.g. AtIPMDH2 and AtIPMDH3). Here we elucidate the molecular basis underlying the metabolic specialization of these enzymes. The 2.25 Å resolution crystal structure of AtIPMDH2 was solved to provide the first detailed molecular architecture of a plant IPMDH. Modeling of 3-isopropylmalate binding in the AtIPMDH2 active site and sequence comparisons of prokaryotic and eukaryotic IPMDH suggest that substitution of one active site residue may lead to altered substrate specificity and metabolic function. Site-directed mutagenesis of Phe-137 to a leucine in AtIPMDH1 (AtIPMDH1-F137L) reduced activity toward 3-(2'-methylthio)ethylmalate by 200-fold, but enhanced catalytic efficiency with 3-isopropylmalate to levels observed with AtIPMDH2 and AtIPMDH3. Conversely, the AtIPMDH2-L134F and AtIPMDH3-L133F mutants enhanced catalytic efficiency with 3-(2'-methylthio)ethylmalate ∼100-fold and reduced activity for 3-isopropylmalate. Furthermore, the altered in vivo glucosinolate profile of an Arabidopsis ipmdh1 T-DNA knock-out mutant could be restored to wild-type levels by constructs expressing AtIPMDH1, AtIPMDH2-L134F, or AtIPMDH3-L133F, but not by AtIPMDH1-F137L. These results indicate that a single amino acid substitution results in functional divergence of IPMDH in planta to affect substrate specificity and contributes to the evolution of specialized glucosinolate biosynthesis from the ancestral leucine pathway.
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Affiliation(s)
- Yan He
- Department of Biology, Genetics Institute, Plant Molecular, and Cellular Biology Program, University of Florida, Gainesville, Florida 32610 and
| | - Ashley Galant
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Qiuying Pang
- Department of Biology, Genetics Institute, Plant Molecular, and Cellular Biology Program, University of Florida, Gainesville, Florida 32610 and
| | - Johanna M Strul
- Department of Biology, Genetics Institute, Plant Molecular, and Cellular Biology Program, University of Florida, Gainesville, Florida 32610 and
| | | | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular, and Cellular Biology Program, University of Florida, Gainesville, Florida 32610 and.
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11
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Gráczer É, Merli A, Singh RK, Karuppasamy M, Závodszky P, Weiss MS, Vas M. Atomic level description of the domain closure in a dimeric enzyme: thermus thermophilus 3-isopropylmalate dehydrogenase. MOLECULAR BIOSYSTEMS 2011; 7:1646-59. [PMID: 21387033 DOI: 10.1039/c0mb00346h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The domain closure associated with the catalytic cycle is described at an atomic level, based on pairwise comparison of the X-ray structures of homodimeric Thermus thermophilus isopropylmalate dehydrogenase (IPMDH), and on their detailed molecular graphical analysis. The structures of the apo-form without substrate and in complex with the divalent metal-ion to 1.8 Å resolution, in complexes with both Mn(2+) and 3-isopropylmalate (IPM), as well as with both Mn(2+) and NADH, were determined at resolutions ranging from 2.0 to 2.5 Å. Single crystal microspectrophotometric measurements demonstrated the presence of a functionally competent protein conformation in the crystal grown in the presence of Mn(2+) and IPM. Structural comparison of the various complexes clearly revealed the relative movement of the two domains within each subunit and allowed the identification of two hinges at the interdomain region: hinge 1 between αd and βF as well as hinge 2 between αh and βE. A detailed analysis of the atomic contacts of the conserved amino acid side-chains suggests a possible operational mechanism of these molecular hinges upon the action of the substrates. The interactions of the protein with Mn(2+) and IPM are mainly responsible for the domain closure: upon binding into the cleft of the interdomain region, the substrate IPM induces a relative movement of the secondary structural elements βE, βF, βG, αd and αh. A further special feature of the conformational change is the movement of the loop bearing the amino acid Tyr139 that precedes the interacting arm of the subunit. The tyrosyl ring rotates and moves by at least 5 Å upon IPM-binding. Thereby, new hydrophobic interactions are formed above the buried isopropyl-group of IPM. 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.
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Affiliation(s)
- Éva Gráczer
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, PO Box 7, H1518 Budapest, Hungary
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12
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Radestock S, Gohlke H. Protein rigidity and thermophilic adaptation. Proteins 2011; 79:1089-108. [DOI: 10.1002/prot.22946] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/28/2010] [Accepted: 11/07/2010] [Indexed: 11/05/2022]
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13
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Merli A, Manikandan K, Gráczer É, Schuldt L, Singh RK, Závodszky P, Vas M, Weiss MS. Crystallization and preliminary X-ray diffraction analysis of various enzyme-substrate complexes of isopropylmalate dehydrogenase from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:738-43. [PMID: 20516614 PMCID: PMC2882784 DOI: 10.1107/s174430911001626x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 05/03/2010] [Indexed: 11/10/2022]
Abstract
The Thermus thermophilus 3-isopropylmalate dehydrogenase (Tt-IPMDH) enzyme catalyses the penultimate step of the leucine-biosynthesis pathway. It converts (2R,3S)-3-isopropylmalate to (2S)-2-isopropyl-3-oxosuccinate in the presence of divalent Mg(2+) or Mn(2+) and with the help of NAD(+). In order to elucidate the detailed structural and functional mode of the enzymatic reaction, crystals of Tt-IPMDH were grown in the presence of various combinations of substrate and/or cofactors. Here, the crystallization, data collection and preliminary crystallographic analyses of six such complexes are reported.
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Affiliation(s)
- Angelo Merli
- Department of Biochemistry and Molecular Biology, University of Parma, Viale G. P. Usberti 23/A, 43100 Parma, Italy
| | | | - Éva Gráczer
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H1518 Budapest, PO Box 7, Hungary
| | - Linda Schuldt
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | - Péter Závodszky
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H1518 Budapest, PO Box 7, Hungary
| | - Mária Vas
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H1518 Budapest, PO Box 7, Hungary
| | - Manfred S. Weiss
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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14
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Nango E, Yamamoto T, Kumasaka T, Eguchi T. Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor. Bioorg Med Chem 2009; 17:7789-94. [PMID: 19833522 DOI: 10.1016/j.bmc.2009.09.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 09/12/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
Isopropylmalate dehydrogenase (IPMDH) is the third enzyme specific to leucine biosynthesis in microorganisms and plants, and catalyzes the oxidative decarboxylation of (2R,3S)-3-isopropylmalate to alpha-ketoisocaproate using NAD(+) as an oxidizing agent. In this study, a thia-analogue of the substrate was designed and synthesized as an inhibitor for IPMDH. The analogue showed strong competitive inhibitory activity with K(i)=62nM toward IPMDH derived from Thermus thermophilus. Moreover, the crystal structure of T. thermophilus IPMDH in a ternary complex with NAD(+) and the inhibitor has been determined at 2.8A resolution. The inhibitor exists as a decarboxylated product with an enol/enolate form in the active site. The product interacts with Arg 94, Asn 102, Ser 259, Glu 270, and a water molecule hydrogen-bonding with Arg 132. All interactions between the product and the enzyme were observed in the position associated with keto-enol tautomerization. This result implies that the tautomerization step of the thia-analogue during the IPMDH reaction is involved in the inhibition.
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Affiliation(s)
- Eriko Nango
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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15
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Hajdú I, Szilágyi A, Kardos J, Závodszky P. A link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase. Biophys J 2009; 96:5003-12. [PMID: 19527660 DOI: 10.1016/j.bpj.2009.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 03/31/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022] Open
Abstract
Enzyme function depends on specific conformational motions. We show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. While investigating the catalytic properties of IPMDH from Escherichia coli, we found that its catalytic efficiency (k(cat)/K(M,IPM)) for the substrate IPM has an unusual temperature dependence, showing a local minimum at approximately 35 degrees C. In search of an explanation, we measured the individual constants k(cat) and K(M,IPM) as a function of temperature, and found that the van 't Hoff plot of K(M,IPM) shows sigmoid-like transition in the 20-40 degrees C temperature range. By means of various measurements including hydrogen-deuterium exchange and fluorescence resonance energy transfer, we showed that the conformational fluctuations, including hinge-bending domain motions increase more steeply with temperatures >30 degrees C. The thermodynamic parameters of ligand binding determined by isothermal titration calorimetry as a function of temperature were found to be strongly correlated to the conformational fluctuations of the enzyme. Because the binding of IPM is associated with a hinge-bending domain closure, the more intense hinge-bending fluctuations at higher temperatures increasingly interfere with IPM binding, thereby abruptly increasing its dissociation constant and leading to the observed unusual temperature dependence of the catalytic efficiency.
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Affiliation(s)
- István Hajdú
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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16
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Sasaki M, Uno M, Akanuma S, Yamagishi A. Random mutagenesis improves the low-temperature activity of the tetrameric 3-isopropylmalate dehydrogenase from the hyperthermophile Sulfolobus tokodaii. Protein Eng Des Sel 2008; 21:721-7. [DOI: 10.1093/protein/gzn054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Imada K, Tamura T, Takenaka R, Kobayashi I, Namba K, Inagaki K. Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity. Proteins 2008; 70:63-71. [PMID: 17634983 DOI: 10.1002/prot.21486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The crystal structure of Acidithiobacillus thiooxidans isocitrate dehydrogenase complexed with NAD+ and citrate has been solved to a resolution of 1.9 A. The protein fold of this NAD+-dependent enzyme shares a high similarity with those of NADP+-dependent bacterial ICDHs. The NAD+ and the citrate are clearly identified in the active site cleft with a well-defined electron density. Asp-357 is the direct cofactor-specificity determinant that interacts with 2'-OH and 3'-OH of the adenosine ribose. The adenosine ribose takes a C2'-endo puckering conformation as previously reported for an NAD+-specific isopropylmalate dehydrogenase. The nicotinamide moiety of NAD+ has the amide NH2 group oriented in cis conformation with respect to the C4 carbon of the nicotinamide ring, slanted toward the bound citrate molecule with a dihedral angle of -21 degrees . The semi-empirical molecular orbital calculation suggests that the pro-R hydrogen atom at C4 of NADH would bear the largest negative charge when the amide NH2 group is in such conformation, suggesting that the amide group has a catalytically significant role in stabilizing the transition state as NADH is being formed during the hydride transfer catalysis.
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Affiliation(s)
- Katsumi Imada
- Department of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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18
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Karsten WE, Cook PF. An isothermal titration calorimetry study of the binding of substrates and ligands to the tartrate dehydrogenase from Pseudomonas putida reveals half-of-the-sites reactivity. Biochemistry 2006; 45:9000-6. [PMID: 16846243 DOI: 10.1021/bi0607251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An isothermal titration calorimetric study of the binding of substrates and inhibitors to different complexes of tartrate dehydrogenase (TDH) from Pseudomonas putida was carried out. TDH catalyzes the nicotinamide adenine dinucleotide (NAD)-dependent oxidative decarboxylation of d-malate and has an absolute requirement for both a divalent and monovalent metal ion for activity. The ligands Mn(2+), meso-tartrate, oxalate, and reduced nicotinamide adenine dinucleotide (NADH) bound to all TDH complexes with a stoichiometry of 1 per enzyme dimer. The exception is NAD, which binds to E/K(+), E/K(+)/Mn(2+), and E/K(+)/Mg(2+) complexes with a stoichiometry of two per enzyme dimer. The binding studies suggest a half-of-the-sites mechanism for TDH. No significant heat changes were observed for d-malate in the presence of the E/K(+)/Mn(2+) complex, suggesting that it did not bind. In contrast, meso-tartrate does bind to E/K(+)/Mn(2+) but gives no significant heat change in the presence of E/Mn(2+), suggesting that K(+) is required for meso-tartrate binding. meso-Tartrate also binds with a large DeltaC(p) value and likely binds via a different binding mode than d-malate, which binds only in the presence of NAD. In contrast to all of the other ligands tested, the binding of Mn(2+) is entropically driven, likely the result of the entropically favored disruption of ordered water molecules coordinated to Mn(2+) in solution that are lost upon binding to the enzyme. Oxalate, a competitive inhibitor of malate, binds with the greatest affinity to E/K(+)/Mn(2+)/NADH, and its binding is associated with the uptake of a proton. Overall, with d-malate as the substrate, data are consistent with a random addition of K(+), Mn(2+), and NAD followed by the ordered addition of d-malate; there is significant synergism in the binding of NAD and K(+). Although the binding of meso-tartrate also requires enzyme-bound K(+) and Mn(2+), the binding of meso-tartrate and NAD is random.
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Affiliation(s)
- William E Karsten
- Department of Chemistry and Biochemistry, Unversity of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA
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Singh RK, Kefala G, Janowski R, Mueller-Dieckmann C, von Kries JP, Weiss MS. The high-resolution Structure of LeuB (Rv2995c) from Mycobacterium tuberculosis. J Mol Biol 2004; 346:1-11. [PMID: 15663922 DOI: 10.1016/j.jmb.2004.11.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2004] [Revised: 11/13/2004] [Accepted: 11/23/2004] [Indexed: 11/17/2022]
Abstract
The crystal structure of the enzyme 3-isopropylmalate dehydrogenase (IPMDH) from Mycobacterium tuberculosis (LeuB, Mtb-IPMDH, Rv2995c) without substrate or co-factor was determined at 1.65 A resolution, which is the highest resolution reported for an IPMDH to date. The crystals contain two functional dimers in the asymmetric unit in an arrangement close to a tetramer of D2 symmetry. Despite the absence of a substrate or inhibitor bound to the protein, the structure of the monomer resembles the previously observed closed form of the enzyme more closely than the open form. A comparison with the substrate complex of IPMDH from Thiobacillus ferrooxidans and the co-factor complex of the Thermus thermophilus enzyme revealed a close relationship of the active-site architecture between the various bacterial enzymes. The inhibitor O-isobutenyl oxalylhydroxamate was found to bind to the active site of IPMDH in a mode similar to the substrate isopropylmalate.
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Affiliation(s)
- Rajesh Kumar Singh
- EMBL Hamburg Outstation, c/o DESY, Notkestr. 85, D-22603 Hamburg, Germany
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20
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Yasutake Y, Watanabe S, Yao M, Takada Y, Fukunaga N, Tanaka I. Crystal structure of the monomeric isocitrate dehydrogenase in the presence of NADP+: insight into the cofactor recognition, catalysis, and evolution. J Biol Chem 2003; 278:36897-904. [PMID: 12855708 DOI: 10.1074/jbc.m304091200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NADP+-dependent monomeric isocitrate dehydrogenase (IDH) from the nitrogen-fixing bacterium Azotobacter vinelandii (AvIDH) is one of members of the beta-decarboxylating dehydrogenase family and catalyzes the dehydration and decarboxylation of isocitrate to yield 2-oxoglutrate and CO2 in the Krebs cycle. We solved the crystal structure of the AvIDH in complex with cofactor NADP+ (AvIDH-NADP+ complex). The final refined model shows the closed form that has never been detected in any previously solved structures of beta-decarboxylating dehydrogenases. The structure also reveals all of the residues that interact with NADP+. The structure-based sequence alignment reveals that these residues were not conserved in any other dimeric NADP+-dependent IDHs. Therefore the NADP+ specificity of the monomeric and dimeric IDHs was independently acquired through the evolutional process. The AvIDH was known to show an exceptionally high turnover rate. The structure of the AvIDH-NADP+ complex indicates that one loop, which is not present in the Escherichia coli IDHs, reliably stabilizes the conformation of the nicotinamide mononucleotide of the bound NADP+ by forming a few hydrogen bonds, and such interactions are considered to be important for the monomeric enzyme to initiate the hydride transfer reaction immediately. Finally, the structure of the AvIDH is compared with that of other dimeric NADP-IDHs. Several structural features demonstrate that the monomeric IDHs are structurally more related to the eukaryotic dimeric IDHs than to the bacterial dimeric IDHs.
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Affiliation(s)
- Yoshiaki Yasutake
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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21
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Karsten WE, Tipton PA, Cook PF. Tartrate dehydrogenase catalyzes the stepwise oxidative decarboxylation of D-malate with both NAD and thio-NAD. Biochemistry 2002; 41:12193-9. [PMID: 12356321 DOI: 10.1021/bi026278g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tartrate dehydrogenase catalyzes the divalent metal ion- and NAD-dependent oxidative decarboxylation of D-malate to yield CO(2), pyruvate, and NADH. The enzyme also catalyzes the metal ion-dependent oxidation of (+)-tartrate to yield oxaloglycolate and NADH. pH-rate profiles and isotope effects were measured to probe the mechanism of this unique enzyme. Data suggest a general base mechanism with likely general acid catalysis in the oxidative decarboxylation of D-malate. Of interest, the mechanism of oxidative decarboxylation of D-malate is stepwise with NAD(+) or the more oxidizing thio-NAD(+). The mechanism does not become concerted with the latter as observed for the malic enzyme, which catalyzes the oxidative decarboxylation of L-malate [Karsten, W. E., and Cook, P. F. (1994) Biochemistry 33, 2096-2103]. It appears the change in mechanism observed with malic enzyme is specific to its transition state structure and not a generalized trait of metal ion- and NAD(P)-dependent beta-hydroxy acid oxidative decarboxylases. The V/K(malate) pH-rate profile decreases at low and high pH and exhibits pK(a) values of about 6.3 and 8.3, while that for V/K(tartrate) (measured from pH 7.5 to pH 9) exhibits a pK(a) of 8.6 on the basic side. A single pK(a) of 6.3 is observed on the acid side of the V(max) pH profile, but the pK(a) seen on the basic side of the V/K pH profiles is not observed in the V(max) pH profiles. Data suggest the requirement for a general base that accepts a proton from the 2-hydroxyl group of either substrate to facilitate hydride transfer. A second enzymatic group is also required protonated for optimum binding of substrates and may also function as a general acid to donate a proton to the enolpyruvate intermediate to form pyruvate. The (13)C isotope effect, measured on the decarboxylation of D-malate using NAD(+) as the dinucleotide substrate, decreases from a value of 1.0096 +/- 0.0006 with D-malate to 1.00787 +/- 0.00006 with D-malate-2-d, suggesting a stepwise mechanism for the oxidative decarboxylation of D-malate. Using thio-NAD(+) as the dinucleotide substrate the (13)C isotope effects are 1.0034 +/- 0.0007 and 1.0027 +/- 0.0002 with D-malate and D-malate-2-d, respectively.
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Affiliation(s)
- William E Karsten
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA
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Suzuki T, Yasugi M, Arisaka F, Oshima T, Yamagishi A. Cold-adaptation mechanism of mutant enzymes of 3-isopropylmalate dehydrogenase from Thermus thermophilus. Protein Eng Des Sel 2002; 15:471-6. [PMID: 12082165 DOI: 10.1093/protein/15.6.471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Random mutagenesis of Thermus thermophilus 3-isopropylmalate dehydrogenase revealed that a substitution of Val126Met in a hinge region caused a marked increase in specific activity, particularly at low temperatures, although the site is far from the binding residues for 3-isopropylmalate and NAD. To understand the molecular mechanism, residue 126 was substituted with one of eight other residues, Gly, Ala, Ser, Thr, Glu, Leu, Ile or Phe. Circular dichroism analyses revealed a decreased thermal stability of the mutants (Delta T ((1/2))= 0-13 degrees C), indicating structural perturbations caused by steric conflict with surrounding residues having larger side chains. Kinetic parameters, k(cat) and K(m) values for isopropylmalate and NAD, were also affected by the mutation, but the resulting k(cat)/K(m) values were similar to that of the wild-type enzyme, suggesting that the change in the catalytic property is caused by the change in free-energy level of the Michaelis complex state relative to that of the initial state. The kinetic parameters and activation enthalpy change (Delta H (double dagger)) showed good correlation with the van der Waals volume of residue 126. These results suggested that the artificial cold adaptation (enhancement of k(cat) value at low temperatures) resulted from the destabilization of the ternary complex caused by the increase in the volume of the residue at position 126.
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Affiliation(s)
- Toshiharu Suzuki
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8501, Japan
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Fujita M, Tamegai H, Eguchi T, Kakinuma K. Novel substrate specificity of designer 3-isopropylmalate dehydrogenase derived from Thermus thermophilus HB8. Biosci Biotechnol Biochem 2001; 65:2695-700. [PMID: 11826966 DOI: 10.1271/bbb.65.2695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Redesigning of an enzyme for a new catalytic reaction and modified substrate specificity was exploited with 3-isopropylmalate dehydrogenase (IPMDH). Point-mutation on Gly-89, which is not in the catalytic site but near it, was done by changing it to Ala, Ser, Val, and Pro, and all the mutations changed the substrate specificity. The mutant enzymes showed higher catalytic efficiency (kcat/Km) than the native IPMDH when malate was used as a substrate instead of 3-isopropylmalate. More interestingly, an additional insertion of Gly between Gly-89 and Leu-90 significantly altered the substrate-specificity, although the overall catalytic activity was decreased. Particularly, this mutant turned out to efficiently accept D-lactic acid, which was not accepted as a substrate by wild-type IPMDH at all. These results demonstrate the opportunity for creating nove,enzymes by modification of amino acid residues that do not directly participate in catalysis, or by insertion of additional residues.
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Affiliation(s)
- M Fujita
- Department of Chemistry, Tokyo Institute of Technology, Japan
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Yasugi M, Suzuki T, Yamagishi A, Oshima T. Analysis of the effect of accumulation of amino acid replacements on activity of 3-isopropylmalate dehydrogenase from Thermus thermophilus. PROTEIN ENGINEERING 2001; 14:601-7. [PMID: 11579229 DOI: 10.1093/protein/14.8.601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A newly selected cold-adapted mutant 3-isopropylmalate dehydrogenase (IPMDH) from a random mutant library was a double mutant containing the mutations I11V and S92F that were found in cold-adapted mutant IPMDHs previously isolated. To elucidate the effect of each mutation on enzymatic activity, I11V and six multiple mutant IPMDHs were constructed and analyzed. All of the multiple mutant IPMDHs were found to be improved in catalytic activity at moderate temperatures by increasing the k(cat) with a simultaneous increase of K(m) for the coenzyme NAD(+). k(cat) was improved by a decrease in the activation enthalpy, DeltaH( not equal). The multiple mutants did not show large reduction in thermal stability, and one of them showed enhanced thermal stability. Mutation from I11 to V was revealed to have a stabilizing effect. Mutants showed increased thermal stability when the mutation I11V was combined. This indicates that it is possible to construct mutants with enhanced thermal stability by combining stabilizing mutation. No additivity was observed for the thermodynamic properties of catalytic reaction in the multiple mutant IPMDHs, implying that the structural changes induced by the mutations were interacting with each other. This indicates that careful and detailed tuning is required for enhancing activity in contrast to thermal stability.
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Affiliation(s)
- M Yasugi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Horinouchi 1432-1, Hachioji, Tokyo 192-0392, Japan
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Suzuki T, Yasugi M, Arisaka F, Yamagishi A, Oshima T. Adaptation of a thermophilic enzyme, 3-isopropylmalate dehydrogenase, to low temperatures. PROTEIN ENGINEERING 2001; 14:85-91. [PMID: 11297666 DOI: 10.1093/protein/14.2.85] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Random mutagenesis coupled with screening of the active enzyme at a low temperature was applied to isolate cold-adapted mutants of a thermophilic enzyme. Four mutant enzymes with enhanced specific activities (up to 4.1-fold at 40 degrees C) at a moderate temperature were isolated from randomly mutated Thermus thermophilus 3-isopropylmalate dehydrogenase. Kinetic analysis revealed two types of cold-adapted mutants, i.e. k(cat)-improved and K(m)-improved types. The k(cat)-improved mutants showed less temperature-dependent catalytic properties, resulting in improvement of k(cat) (up to 7.5-fold at 40 degrees C) at lower temperatures with increased K(m) values mainly for NAD. The K(m)-improved enzyme showed higher affinities toward the substrate and the coenzyme without significant change in k(cat) at the temperatures investigated (30-70 degrees C). In k(cat)-improved mutants, replacement of a residue was found near the binding pocket for the adenine portion of NAD. Two of the mutants retained thermal stability indistinguishable from the wild-type enzyme. Extreme thermal stability of the thermophilic enzyme is not necessarily decreased to improve the catalytic function at lower temperatures. The present strategy provides a powerful tool for obtaining active mutant enzymes at lower temperatures. The results also indicate that it is possible to obtain cold-adapted mutant enzymes with high thermal stability.
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Affiliation(s)
- T Suzuki
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8503, Japan
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26
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Hirose R, Suzuki T, Moriyama H, Sato T, Yamagishi A, Oshima T, Tanaka N. Crystal structures of mutants of Thermus thermophilus IPMDH adapted to low temperatures. PROTEIN ENGINEERING 2001; 14:81-4. [PMID: 11297665 DOI: 10.1093/protein/14.2.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Random mutagenesis on thermophilic 3-isopropylmalate dehydrogenases (IPMDH; EC 1.1.1.85) produced mutant enzymes which adapt to low temperatures. These mutants had higher activity at lower temperatures than the wild-type enzyme without losing high thermostability. Here we report three structures of the mutants of Thermus thermophilus IPMDH determined by X-ray diffraction which was adapted to a low-temperature environment. Two of them have unstable coenzyme binding states and the other one probably has a stable substrate binding state. The present research suggests that the adaptation is correlated with the binding of either coenzyme or the substrate.
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Affiliation(s)
- R Hirose
- Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8501, Japan
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27
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Fujita M, Toyooka Y, Tamegai H, Eguchi T, Kakinuma K. Arg-94 is crucial to the catalysis of 3-isopropylmalate dehydrogenase from Thermus thermophilus HB8. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00091-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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28
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Nurachman Z, Akanuma S, Sato T, Oshima T, Tanaka N. Crystal structures of 3-isopropylmalate dehydrogenases with mutations at the C-terminus: crystallographic analyses of structure-stability relationships. PROTEIN ENGINEERING 2000; 13:253-8. [PMID: 10810156 DOI: 10.1093/protein/13.4.253] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Thermal stability of the Thermus thermophilus isopropylmalate dehydrogenase enzyme was substantially lost upon the deletion of three residues from the C-terminus. However, the stability was partly recovered by the addition of two, four and seven amino acid residues (called HD177, HD708 and HD711, respectively) to the C-terminal region of the truncated enzyme. Three structures of these mutant enzymes were determined by an X-ray diffraction method. All protein crystals belong to space group P2(1) and their structures were solved by a standard molecular replacement method where the original dimer structure of the A172L mutant was used as a search model. Thermal stability of these mutant enzymes is discussed based on the 3D structure with special attention to the width of the active-site groove and the minor groove, distortion of beta-sheet pillar structure and size of cavity in the domain-domain interface around the C-terminus. Our previous studies revealed that the thermal stability of isopropylmalate dehydrogenase increases when the active-site cleft is closed (the closed form). In the present study it is shown that the active-site cleft can be regulated by open-close movement of the minor groove located at the opposite side to the active-site groove on the same subunit, through a paperclip-like motion.
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Affiliation(s)
- Z Nurachman
- Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8501, Japan
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Cherbavaz DB, Lee ME, Stroud RM, Koshland DE. Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. J Mol Biol 2000; 295:377-85. [PMID: 10623532 DOI: 10.1006/jmbi.1999.3195] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isocitrate dehydrogenase catalyses the two step, acid base, oxidative decarboxylation of isocitrate to alpha-ketoglutarate. Lysine 230 was suggested to act as proton donor based on geometry and spatial proximity to isocitrate. To clarify further the role of lysine 230, we co-crystallized the lysine-to-methionine mutant (K230M) with isocitrate and with alpha-ketoglutarate. Crystals were flash-frozen and the two structures were determined and refined to 2. 1 A. Several new features were identified relative to the wild-type structure. Seven side-chains previously unplaced in the wild-type structure were identified and included in the model, and the amino acid terminus was extended by an alanine residue. Many additional water molecules were identified. Examination of the K230M active sites (K230M isocitrate and K230M-ketoglutarate) revealed that tyrosine 160 protrudes further into the active site in the presence of either isocitrate or alpha-ketoglutarate in K230 M than it does in the wild-type structure. Also, methionine 230 was not as fully extended, and asparagine 232 rotates approximately 30 degrees toward the ligand permitting polar interactions. Outside the active site cleft a tetragonal volume of density was identified as a sulfate molecule. Its location and interactions suggest it may influence the equilibrium between the tetragonal and the orthorhombic forms of isocitrate dehydrogenase. Differences observed in the active site water structure between the wild-type and K230M structures were due to a single point mutation. A water molecule was located in the position equivalent to that occupied by the wild-type epsilon-amine of lysine 230; a water molecule in that location in K230M suggests it may influence catalysis in the mutant. Comparison of K230M complexed with isocitrate and alpha-ketoglutarate illuminates the influence a ligand has on active site water structure.
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Affiliation(s)
- D B Cherbavaz
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA, 94143-0448, USA
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Chiba A, Arai N, Eguchi T, Kakinuma K. 3-Isopropylidenemalic Acid: A Mechanism-based Inhibitor of 3-Isopropylmalate Dehydrogenase. CHEM LETT 1999. [DOI: 10.1246/cl.1999.1313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Karsten WE, Chooback L, Liu D, Hwang CC, Lynch C, Cook PF. Mapping the active site topography of the NAD-malic enzyme via alanine-scanning site-directed mutagenesis. Biochemistry 1999; 38:10527-32. [PMID: 10441149 DOI: 10.1021/bi9906165] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NAD-malic enzyme cDNA has been subcloned into the pQE expression vector, expressed with a six-His tag, and purified. The His-tagged enzyme is purified by a combination of Ni-NTA and orange A agarose column chromatography with a yield of 45% and an estimated purity of >90%. The tag and linker have no effect on the kinetic parameters of the enzyme compared to the wild-type enzyme. Alanine-scanning site-directed mutagenesis has been carried out on all of the conserved neutral acid residues of the NAD-malic enzyme from Ascaris suum. Data obtained confirm the predicted role of D178 and D295 in metal ion binding, the likely role of D294, D361, and E440 in the NAD binding site, and the role of E58 and D272 in malate binding. Decreases in V/E(t) by 10(4)-fold and in V/K(malate)E(t) by 10(7)-fold, when D295 is changed to alanine, suggest that it is a likely candidate for the general base that accepts a proton from the malate hydroxyl in the oxidation step.
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Affiliation(s)
- W E Karsten
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, USA
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Chiba A, Aoyama T, Suzuki R, Eguchi T, Oshima T, Kakinuma K. Synthetic and Mechanistic Studies of (2R,3S)-3-Vinylmalic Acid as a Mechanism-Based Inhibitor of 3-Isopropylmalate Dehydrogenase. J Org Chem 1999. [DOI: 10.1021/jo982206c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Chiba
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Tetsuya Aoyama
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Rieko Suzuki
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Tairo Oshima
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Katsumi Kakinuma
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
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33
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Chiba A, Eguchi T, Oshima T, Kakinuma K. Synthesis of cyclopropane substrate analog for 3-isopropylmalate dehydrogenase and its mechanism-based inhibition. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00074-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Motono C, Yamagishi A, Oshima T. Urea-induced unfolding and conformational stability of 3-isopropylmalate dehydrogenase from the Thermophile thermus thermophilus and its mesophilic counterpart from Escherichia coli. Biochemistry 1999; 38:1332-7. [PMID: 9930995 DOI: 10.1021/bi982380v] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To reveal the basis of the thermal stability of 3-isopropylmalate dehydrogenase (IPMDH) from an extreme thermophile, Thermus thermophilus, urea-induced unfolding of the enzyme and of its mesophilic counterpart from Escherichia coli has been studied. The urea-induced equilibrium unfolding of T. thermophilus and E. coli IPMDHs at 27 degreesC was monitored by measuring the changes in far-UV CD, intrinsic fluorescence, anilinonaphthalenesulfonic acid (ANS) binding, and catalytic activity in the presence of nonionic detergent Tween 20. For both enzymes, the spectral methods revealed a biphasic unfolding transition. The first transition was protein concentration-independent, whereas the second was protein concentration-dependent for both enzymes. The observation suggested a three-state unfolding mechanism with a dimeric intermediate. However, the intermediates of the E. coli and the T. thermophilus IPMDHs seemed to be different from each other. The intermediate of the E. coli IPMDH lost its secondary and tertiary structure more than that of the thermophilic enzyme. E. coli IPMDH lost enzymatic activity through the transition from the native to the intermediate state, though the intermediate of the T. thermophilus enzyme was still active. The unfolding process of E. coli IPMDH can be explained by a sequential unfolding of individual folding domains, while there is only a small structural perturbation in the intermediate of T. thermophilus IPMDH. The higher thermal stability of T. thermophilus IPMDH can be attributed to the increase in the extent of interaction inside the first domain which unfolded prior to the unfolding of the whole molecular structure in E. coli IPMDH.
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Affiliation(s)
- C Motono
- Department of Molecular Biology, Tokyo University of Pharmacy & Life Science, 1432 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K. Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism. Structure 1998; 6:971-82. [PMID: 9739088 DOI: 10.1016/s0969-2126(98)00099-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. RESULTS We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 A resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the gamma-isopropyl group. The gamma group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. CONCLUSIONS A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C gamma atoms of Glu88 interact with the gamma-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.
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Affiliation(s)
- K Imada
- International Institute for Advanced Research, Matsushita Electric Industrial Co., Ltd., Seika, Japan.
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Závodszky P, Kardos J, Petsko GA. Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc Natl Acad Sci U S A 1998; 95:7406-11. [PMID: 9636162 PMCID: PMC22632 DOI: 10.1073/pnas.95.13.7406] [Citation(s) in RCA: 419] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
3-Isopropylmalate dehydrogenase (IPMDH, E.C. 1.1.1.85) from the thermophilic bacterium Thermus thermophilus HB8 is homologous to IPMDH from the mesophilic Escherichia coli, but has an approximately 17 degreesC higher melting temperature. Its temperature optimum is 22-25 degreesC higher than that of the E. coli enzyme; however, it is hardly active at room temperature. The increased conformational rigidity required to stabilize the thermophilic enzyme against heat denaturation might explain its different temperature-activity profile. Hydrogen/deuterium exchange studies were performed on this thermophilic-mesophilic enzyme pair to compare their conformational flexibilities. It was found that Th. thermophilus IPMDH is significantly more rigid at room temperature than E. coli IPMDH, whereas the enzymes have nearly identical flexibilities under their respective optimal working conditions, suggesting that evolutionary adaptation tends to maintain a "corresponding state" regarding conformational flexibility. These observations confirm that conformational fluctuations necessary for catalytic function are restricted at room temperature in the thermophilic enzyme, suggesting a close relationship between conformational flexibility and enzyme function.
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Affiliation(s)
- P Závodszky
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Pf. 7, H-1518 Budapest, Hungary
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Matsunami H, Kawaguchi H, Inagaki K, Eguchi T, Kakinuma K, Tanaka H. Overproduction and substrate specificity of 3-isopropylmalate dehydrogenase from Thiobacillus ferrooxidans. Biosci Biotechnol Biochem 1998; 62:372-3. [PMID: 9532798 DOI: 10.1271/bbb.62.372] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We constructed an overexpression system in Escherichia coli of the leuB gene coding for 3-isopropylmalate dehydrogenase in Thiobacillus ferrooxidans. E. coli harboring the plasmid we constructed, pKK leuB1, produced 17-fold the enzyme protein of the expression system previously used for purification. The substrate specificity of the enzyme was analyzed with synthetic (2R, 3S)-3-alkylmalates. The 3-isopropylmalate dehydrogenase of Thiobacillus ferrooxidans had broad specificity toward the alkylmalates.
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Affiliation(s)
- H Matsunami
- Department of Bioresources Chemistry, Faculty of Agriculture, Okayama University, Japan
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Finer-Moore J, Tsutakawa SE, Cherbavaz DR, LaPorte DC, Koshland DE, Stroud RM. Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting. Biochemistry 1997; 36:13890-6. [PMID: 9374867 DOI: 10.1021/bi9711691] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To clarify further the mechanism of regulation by phosphorylation of isocitrate dehydrogenase, cocrystallization of isocitrate dehydrogenase and isocitrate dehydrogenase kinase/phosphatase in the presence of an ATP analog was attempted. Although cocrystallization was unsuccessful, a new crystal form of isocitrate dehydrogenase was obtained which provides insight into the phosphorylation mechanism. The new, orthorhombic crystal form of isocitrate dehydrogenase is related to the previously reported tetragonal form largely by an approximately 16 degrees shift of a large domain relative to the small domain and clasp region within each subunit of the dimeric enzyme. The NADP+ cofactor binding surface is significantly disrupted by the shift to the open conformation. The solvent-accessible surface area and surface-enclosed volume increase by 2% relative to the dimeric tetragonal form. Most of the increase results from expansion of the active site cleft such that the distance across its opening increases from approximately 5 to 13 A, significantly increasing accessibility to Ser-113. The conformation of isocitrate dehydrogenase in the orthorhombic crystal form more closely resembles that of the crystal structure of the homologous enzyme 3-isopropylmalate dehydrogenase than does the tetragonal isocitrate dehydrogenase conformation. Since the crystal lattice forces are fairly weak, it appears that isocitrate dehydrogenase is a flexible molecule that can easily undergo domain shifts and possibly other induced fit conformational changes, to accommodate binding to isocitrate dehydrogenase kinase/phosphatase.
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Affiliation(s)
- J Finer-Moore
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA
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39
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Wallon G, Kryger G, Lovett ST, Oshima T, Ringe D, Petsko GA. Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. J Mol Biol 1997; 266:1016-31. [PMID: 9086278 DOI: 10.1006/jmbi.1996.0797] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The basis of protein stability has been investigated by the structural comparison of themophilic enzymes with their mesophilic counterparts. A number of characteristics have been found that can contribute to the stabilization of thermophilic proteins, but no one is uniquely capable of imparting thermostability. The crystal structure of 3-isopropylmalate dehydrogenase (IPMDH) from the mesophiles Escherichia coli and Salmonella typhimurium have been determined by the method of molecular replacement using the known structure of the homologous Thermus thermophilus enzyme. The structure of the E. coli enzyme was refined at a resolution of 2.1 A to an R-factor of 17.3%, that of the S. typhimurium enzyme at 1.7 A resolution to an R-factor of 19.8%. The three structures were compared to elucidate the basis of the higher thermostability of the T. thermophilus enzyme. A mutant that created a cavity in the hydrophobic core of the thermophilic enzyme was designed to investigate the importance of packing density for thermostability. The structure of this mutant was analyzed. The main stabilizing features in the thermophilic enzyme are an increased number of salt bridges, additional hydrogen bonds, a proportionately larger and more hydrophobic subunit interface, shortened N and C termini and a larger number of proline residues. The mutation in the hydrophobic core of T. thermophilus IPMDH resulted in a cavity of 32 A3, but no significant effect on the activity and thermostability of the mutant was observed.
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Affiliation(s)
- G Wallon
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254-9910, USA
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40
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Synthesis of conformationally restricted substrate analogs and their interaction with 3-isopropylmalate dehydrogenase derived from Thermus thermophilus. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(97)00104-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Suzuki T, Inoki Y, Yamagishi A, Iwasaki T, Wakagi T, Oshima T. Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Bacteriol 1997; 179:1174-9. [PMID: 9023199 PMCID: PMC178813 DOI: 10.1128/jb.179.4.1174-1179.1997] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The archaeal leuB gene encoding isopropylmalate dehydrogenase of Sulfolobus sp. strain 7 was cloned, sequenced, and expressed in Escherichia coli. The recombinant Sulfolobus sp. enzyme was extremely stable to heat. The substrate and coenzyme specificities of the archaeal enzyme resembled those of the bacterial counterparts. Sedimentation equilibrium analysis supported an earlier proposal that the archaeal enzyme is homotetrameric, although the corresponding enzymes studied so far have been reported to be dimeric. Phylogenetic analyses suggested that the archaeal enzyme is homologous to mitochondrial NAD-dependent isocitrate dehydrogenases (which are tetrameric or octameric) as well as to isopropylmalate dehydrogenases from other sources. These results suggested that the present enzyme is the most primitive among isopropylmalate dehydrogenases belonging in the decarboxylating dehydrogenase family.
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Affiliation(s)
- T Suzuki
- Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
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Yaoi T, Hayashi-Iwasaki Y, Oshima T. Electrostatic interaction between two domains of isocitrate dehydrogenase from Thermus thermophilus is important for the catalytic function and protein stability. FEBS Lett 1996; 398:228-30. [PMID: 8977112 DOI: 10.1016/s0014-5793(96)01243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The role of electrostatic interaction between Lys96 and Glu147 of isocitrate dehydrogenase from Thermus thermophilus was investigated by site-directed mutagenesis. These two residues are located near the active site and involved in the interdomain interaction. Analyses of the catalytic properties and thermostability of the Glu147Gln mutant revealed that this interaction plays important roles in catalytic function and protein stability.
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Affiliation(s)
- T Yaoi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Japan
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