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Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, H-1117, Hungary
Dipartimento di Bioscienze, Universitá Degli Studi di Parma, Parma, Italy
Helmholtz Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert Einstein Straße 15, Berlin, D-12489, Germany
Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Brussels, B-1050, Belgium
Brussels Center for Redox Biology, Brussels, B-1050, Belgium
Structural Biology Brussels Laboratory, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
Cited By :12
Export Date: 15 April 2021
CODEN: FJEOA
Correspondence Address: Weiss, M.S.; Helmholtz Zentrum Berlin für Materialien und Energie, Albert Einstein Straße 15, Germany; email: manfred.weiss@helmholtz-berlin.de
Chemicals/CAS: 3 isopropylmalate dehydrogenase, 9030-97-1; magnesium, 7439-95-4; manganese, 16397-91-4, 7439-96-5; nicotinamide adenine dinucleotide, 53-84-9; potassium, 7440-09-7; 3-Isopropylmalate Dehydrogenase; Bacterial Proteins; Magnesium; Malates; Manganese; NAD; Potassium
Funding details: Hungarian Scientific Research Fund, OTKA, 108642
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The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn2+, 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.
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<div class="title"><a href="/gui2/?mode=browse¶ms=publication;2785761" target="_blank">Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis</a></div> <div> <span class="journal-title">FEBS JOURNAL</span>
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<pre class="comment" style="margin-top: 0; margin-bottom: 0;"><u>Comments</u>: Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt....</pre>
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/api/publication/2339846
<div class="JournalArticle Publication short-list"> <div class="authors"> <span class="author-name" mtid="10013951"> <a href="/gui2/?type=authors&mode=browse&sel=10013951" target="_blank">Graczer, Eva</a> </span> <span class="author-type"> </span> ; <span class="author-name" > Lionne, Corinne </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10000346"> <a href="/gui2/?type=authors&mode=browse&sel=10000346" target="_blank">Zavodszky, Peter</a> </span> <span class="author-type"> </span> ; <span class="author-name" > Chaloin, Laurent </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10009409"> <a href="/gui2/?type=authors&mode=browse&sel=10009409" target="_blank">Vas, Maria</a> </span> <span class="author-type"> </span> </div ><div class="title"><a href="/gui2/?mode=browse¶ms=publication;2339846" mtid="2339846" target="_blank">Transient kinetic studies reveal isomerization steps along the kinetic pathway of Thermusthermophilus 3-isopropylmalate dehydrogenase</a></div> <div class="pub-info"> <span class="journal-title">FEBS JOURNAL</span> <span class="journal-volume">280</span> : <span class="journal-issue">8</span> <span class="page"> pp. 1764-1772. , 9 p. </span> <span class="year">(2013)</span> </div> <div class="pub-end"><div class="identifier-list"> <span class="identifiers"> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="10.1111/febs.12191" target="_blank" href="https://doi.org/10.1111/febs.12191"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:black" title="4364" target="_blank" href="http://real.mtak.hu/4364"> REAL </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000317609000003" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000317609000003"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="84876296940" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-84876296940"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:black" title="23421786" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=23421786&dopt=Abstract"> PubMed </a> </span> </span> </div> <div class="short-pub-prop-list"> <span class="short-pub-mtid"> Publication:2339846 </span> <span class="status-holder"><span class="status-data status-ADMIN_APPROVED"> Admin approved </span></span> <span class="pub-core">Core Citing </span> <span class="pub-type">Journal Article (Article ) </span> <!-- && !record.category.scientific --> <span class="pub-category">Scientific</span> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="" class="citingPub-count">Citing papers: 7</span> | Independent citation: 4 | Self citation: 3 | Unknown citation: 0 | Number of citations in WoS: 7 | Number of citations in Scopus: 6 | WoS/Scopus assigned: 7 | Number of citations with DOI: 6 </div> </div> </div> </div><div class="JournalArticle Publication long-list">
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<img title="Forrásközlemény" style="float: left" src="/frontend/resources/grid/publication-core-icon.png">
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<div class="autype autype0"> <span class="author-name" mtid="10013951"><a
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(<span class="authorship-author-name">Gráczer Éva Laura</span>
<span class="authorAux-mtmt"> Enzimológia</span>)
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<span class="author-affil"><span title="MTA Research Centre for Natural Sciences">MTA TTK</span>/Institute of Enzymology</span>
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<span class="author-name" >Lionne Corinne
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<span class="author-name" mtid="10000346"><a
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<span class="authorAux-mtmt"> Molekuláris immunológia, biokémia</span>)
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<span class="author-affil"><span title="MTA Research Centre for Natural Sciences">MTA TTK</span>/Institute of Enzymology</span>
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<span class="author-name" >Chaloin Laurent
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;
<span class="author-name" mtid="10009409"><a
href="/gui2/?type=authors&mode=browse&sel=10009409" target="_blank">Vas Maria
(<span class="authorship-author-name">Kazinczyné Vas Mária</span>
<span class="authorAux-mtmt"> Enzimológia</span>)
</a>
</span>
<span class="author-affil"><span title="MTA Research Centre for Natural Sciences">MTA TTK</span>/Institute of Enzymology</span>
</div>
</div>
<div class="title"><a href="/gui2/?mode=browse¶ms=publication;2339846" target="_blank">Transient kinetic studies reveal isomerization steps along the kinetic pathway of Thermusthermophilus 3-isopropylmalate dehydrogenase</a></div> <div> <span class="journal-title">FEBS JOURNAL</span>
<span class="journal-issn">(<a target="_blank" href="https://portal.issn.org/resource/ISSN/1742-464X">1742-464X</a> <a target="_blank" href="https://portal.issn.org/resource/ISSN/1742-4658">1742-4658</a>)</span>:
<span class="journal-volume">280</span> <span class="journal-issue">8</span>
<span class="page">
pp 1764-1772
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<span class="language" xmlns="http://www.w3.org/1999/html">Language:
English
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<div class="publication-citation" style="margin-left: 0.5cm;">
<span title="" class="citingPub-count">Citing papers: 7</span>
| Independent citation: 4
| Self citation: 3
| Unknown citation: 0
| Number of citations in WoS: 7
| Number of citations in Scopus: 6
| WoS/Scopus assigned: 7
| Number of citations with DOI: 6
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<div class="publication-citation">
<a target="_blank" href="/api/publication?cond=citations.related;eq;2339846&sort=publishedYear,desc&sort=title">
Number of cited publications: 8
</a>
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<div class="mtid"><span class="long-pub-mtid">Publication: 2339846</span>
| <span class="status-data status-ADMIN_APPROVED"> Admin approved
</span>
<span class="oldId">Old id: 2339846</span> |
Core Citing
| <span class="type-subtype">Journal Article
( Article
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| <span class="pub-category">Scientific</span>
| <span class="publication-sourceOfData">WOS</span>
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<div class="lastModified">Last Modified: 2020.12.05. 16:39 import WoS (admin)
</div>
<pre class="comment" style="margin-top: 0; margin-bottom: 0;"><u>Comments</u>: Megjegyzés-23169602
N1 : Chemicals/CAS3 isopropylmalate dehydrogenase, 9030-97-1; magnesium ion, 22537-22-0; reduced nicotinamide adenine dinucleotide, 58-68-4; tryptophan, 6912-86-3, 73-22-3
Megjegyzés-23169791
N1 : Chemicals/CAS3 isopropylmalate dehydrogenase, 9030-97-1; magnesium ion, 22537-22-0; reduced nicotinamide adenine dinucleotide, 58-68-4; tryptophan, 6912-86-3, 73-22-3
Megjegyzés-23...</pre>
</div></div>