PDB-101: Molecule of the Month: Pyruvate Dehydrogenase Complex

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overflow-wrap: break-word; } div.jmol-image { margin-bottom: 5px; } </style> <script> // jmol script var jmolLoaded = false function loadIframe() { if (jmolLoaded == false) { var src = '/motm/jmol/?id=' + 153 console.log('src=' + src) $("#iframe").attr('src', src) jmolLoaded = true } } function clickJmolTab() { $('#jmol-tab').trigger('click') } // jmol script for legacy motms with multiple jmols var jmols = []; function loadIframeById(jmolId) { var jmol = jmols[jmolId - 1] if (jmol.loaded == false) { var src = '/motm/jmol/?id=' + 153 + '&jmolId=' + jmolId $("#iframe_" + jmolId).attr('src', src) jmol.loaded = true } } function clickJmolTab(i) { var j = i + 1 $('#jmol-tab-' + j).trigger('click') } </script> <div id="sub-navbar"> <div class="row hidden-print"> <div class="col-xs-12 col-sm-6 sub-navbar"> <h4>Molecule of the Month</h4> </div> <div class="col-xs-12 col-sm-6 text-right sub-navbar"> <table> <tr> <td onclick="location.href="/motm/motm-by-category"">By Category</td> <td onclick="location.href="/motm/motm-by-date"">By Date</td> <td onclick="location.href="/motm/motm-by-title"">By Title</td> </tr> </table> </div> </div> </div> <div data-elastic-include> <h1>Molecule of the Month: Pyruvate Dehydrogenase Complex</h1> <p><i>A huge molecular complex links three sequential reactions for energy production</i></p> <div> <div class="img-with-caption float-left"> <div class="img-with-caption-table"><img src="https://cdn.rcsb.org/pdb101/motm/153/153-PyruvateDehydrogenaseComplex_pyruvatedehydrogenase.jpg" alt="Pyruvate dehydrogenase complex. Flexible linkers, which are not included in the atomic coordinates, are shown schematically." class="img-responsive"> <div class="img-caption"> <div style="margin-bottom:10px;"><i>Pyruvate dehydrogenase complex. Flexible linkers, which are not included in the atomic coordinates, are shown schematically.</i></div><a href="https://cdn.rcsb.org/pdb101/motm/153/153-PyruvateDehydrogenaseComplex_pyruvatedehydrogenase.tif"><small>Download high quality TIFF image<span class="fa fa-cloud-download"></span></small></a> </div> </div> </div> <h4>Introduction</h4> <div>A combination of crystallography, NMR spectroscopy and electron microscopy is revealing the secrets of pyruvate dehydrogenase complex. The complex performs a central step in energy production, catalyzing the reaction that links glycolysis with the tricarboxylic acid cycle. The reaction is performed in three separate steps by three separate enzymes, but all three enzymes are linked efficiently together into one large multienzyme complex.</div> <h4>Anatomy of a Multienzyme Complex</h4> <div>The complex has many moving parts that work together to perform the overall reaction. It is built around a symmetrical core, shown here in blue. Each of the protein chains in this core has a long flexible tail which folds into several additional functional domains. One of these domains grabs the other enzymes in the complex, shown in green and yellow/pink. There are also several small domains that act as carriers. A lysine amino acid on these domains (shown in magenta) is attached to a special carrier molecule, lipoic acid (not included in the structure). It delivers the molecule being broken down from enzyme to enzyme during the reaction. Note that this illustration is highly simplified: only 6 of the 24 tails are shown. In the actual complex, the center core is completely surrounded.</div> <h4>Uncovering the Complex</h4> <div>Since the overall complex is so flexible, it has been difficult to study. Structural biologists have taken a divide-and-conquer approach, and broken the complex into small pieces that are amenable for study. Pictures of the whole complex from electron microscopy are then used to figure out how to reassemble all the pieces. Several structures are included in this illustration: the central core (<span class="rcsb_id_tag" title="Pyruvate Dehydrogenase Complex"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1eaa' target='_blank'>1eaa <i class='fa fa-external-link'> </i></a></span>), the carrier domains (<span class="rcsb_id_tag" title="Pyruvate Dehydrogenase Complex"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1lac' target='_blank'>1lac <i class='fa fa-external-link'> </i></a></span>), and two enzymes bound to the linker domains of the flexible tail (<span class="rcsb_id_tag" title="Pyruvate Dehydrogenase Complex"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1w85' target='_blank'>1w85 <i class='fa fa-external-link'> </i></a></span>and <span class="rcsb_id_tag" title="Pyruvate Dehydrogenase Complex"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1ebd' target='_blank'>1ebd <i class='fa fa-external-link'> </i></a></span>).</div> </div> <div class="clearfix"></div> <hr class="motm-hr"> <div> <div class="img-with-caption float-left"> <div class="img-with-caption-table"><img src="https://cdn.rcsb.org/pdb101/motm/153/153-PyruvateDehydrogenaseComplex_1w85_composite.jpg" alt="E1 subunit of pyruvate dehydrogenase (right) and thiamine pyrophosphate (left)." class="img-responsive"> <div class="img-caption"> <div style="margin-bottom:10px;"><i>E1 subunit of pyruvate dehydrogenase (right) and thiamine pyrophosphate (left).</i></div><a href="https://cdn.rcsb.org/pdb101/motm/153/153-PyruvateDehydrogenaseComplex_1w85_composite.tif"><small>Download high quality TIFF image<span class="fa fa-cloud-download"></span></small></a> </div> </div> </div> <h4>Take Your Vitamins!</h4> <div>The reactions performed in this complex are tricky, so several specialized chemical tools are used by the enzymes. The enzyme that performs the first step, shown here from PDB entry <span class="rcsb_id_tag" title="Pyruvate Dehydrogenase Complex"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1w85' target='_blank'>1w85 <i class='fa fa-external-link'> </i></a></span>, uses thiamine pyrophosphate to extract carbon dioxide from pyruvate. The thiamine molecule has a particularly reactive carbon atom, shown here with a star, which assists with the reaction. Other chemical tools are also needed in the complex: the little carrier domains need lipoic acid to hold tightly to the acetyl groups that are produced by the first enzyme, and they ultimately transfer them to another unusual chemical carrier molecule: coenzyme A. The enzyme that performs the last step requires FAD and NAD to perform a restorative reaction on the lipoic acid. Our cells are not able to build several of these complicated chemical tools from scratch, so we need to obtain these molecules as the vitamins thiamine, pantothenic acid, riboflavin and niacin in our diet.</div> </div> <div class="clearfix"></div> <hr class="motm-hr"> <h4>Exploring the Structure</h4> <div id="jmolTabs" class="jmolText"> <ul class="nav nav-tabs"> <li class="active"><a data-toggle="tab" href="#tabs-1">Image</a></li> <li><a id="jmol-tab" data-toggle="tab" href="#tabs-2" onclick="loadIframe();">JSmol</a></li> </ul> <div class="tab-content"> <div id="tabs-1" class="tab-pane active"> <h5>Pyruvate Dehydrogenase (PDB entries 1eaa and 1b5s)</h5> <div style="margin-top:0;" class="img-with-caption float-left"><img src="https://cdn.rcsb.org/pdb101/motm/153/153-PyruvateDehydrogenaseComplex_1b5s_jmol.jpg" onclick="clickJmolTab();" class="img-responsive"></div> <p>As is often the case in biology, things get even more complicated when you look closer. There are many variations on this basic structure in different types of cells. Some cells have one or two carrier domains on the little tails instead of the three shown here. The complex in our cells also includes another protein in the core, with its own carrier domains. Also, the core itself can have different geometry: a cube-shaped core composed of 24 subunits or a dodecahedral core composed of 60 subunits (shown here from PDB entry <span class="rcsb_id_tag" title="Pyruvate Dehydrogenase Complex"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1b5s' target='_blank'>1b5s <i class='fa fa-external-link'> </i></a></span>). To explore both of these types of cores, click on the image for an interactive Jmol.</p> <div class="clearfix"></div> </div> <div id="tabs-2" class="tab-pane"> <iframe id="iframe" marginheight="0" marginwidth="0" scrolling="yes" frameborder="0" width="100%"></iframe> </div> </div> </div> <div class="row"> <div class="col-xs-12 col-sm-12 col-md-6"> <h4>Topics for Further Discussion</h4> <ol> <li>More and more proteins are being discovered that include several functional </li> <li>domains connected by flexible linkers. Can you find other examples in the PDB?</li> <li>In the PDB, you can find many different enzymes that use cofactors derived from </li> <li>vitamins such as thiamine, niacin, and riboflavin. Do they all perform similar </li> <li>functions, or are the cofactors used in different ways?</li> <li>More and more proteins are being discovered that include several functional </li> <li>domains connected by flexible linkers. Can you find other examples in the PDB?</li> <li>In the PDB, you can find many different enzymes that use cofactors derived from </li> <li>vitamins such as thiamine, niacin, and riboflavin. Do they all perform similar </li> <li>functions, or are the cofactors used in different ways?</li> </ol> <div data-elastic-exclude> <div class="col-xs-12 link-motm"> <h4>Related PDB-101 Resources</h4> <ul> <li>Browse <a href="/browse/biological-energy">Biological Energy</a></li> <li>Browse <a href="/browse/enzymes">Enzymes</a></li> <li>Browse <a href="/browse/peak-performance">Peak Performance</a></li> </ul> </div> </div> </div> <div style="border-left:1px dashed #ddd;" class="col-xs-12 col-sm-12 col-md-6"> <h4>References</h4> <ol> <li>D. L. Nelson and M. M. Cox (2008) Lehninger Principles of Biochemistry. Worth </li> <li>Publishers, New York.</li> <li>X. Yu, Y. Hiromasa, H. Tsen, J. K. Stoops, T. E. Roche and Z. H. Zhou (2008) Structures </li> <li>of the human pyruvate dehydrogeanse complex cores: a highly conserved catalytic </li> <li>center with flexible N-terminal domains. Structure 16, 104-114.</li> <li>J. L. S. Milne, X. Wu, M. J. Borgnia, J. S. Lengyel, B. R. Brooks, D. Shi, R. N. Perham and </li> <li>S. Subramaniam (2006) Molecular structure of a 9-MDa icosahedral pyruvate </li> <li>dehydroegnase subcomplex containing the E2 and E3 enzymes using cryoelectron </li> <li>microscopy. Journal of Biological Chemistry 281. 4364-4370</li> <li>T. Izard, A. Aevarsson, M. D. Allen, A. H. Westphal, R. N. Perham, A. deKok and W. G. J. </li> <li>Hol (1999) Principles of quasi-equivalence and Euclidean geometry govern the </li> <li>assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes. </li> <li>Proceedings of the National Academy of Sciences USA 96, 1240-1245.</li> </ol> </div> </div> <hr class="motm-hr"> <p>September 2012, David Goodsell</p> <a href="http://doi.org/10.2210/rcsb_pdb/mom_2012_9">http://doi.org/10.2210/rcsb_pdb/mom_2012_9</a> </div> <div style="margin-top:20px;" class="row hidden-print"> <div class="col-xs-12"> <div class="panel panel-info"> <div class="panel-heading">About Molecule of the Month</div> <div class="panel-body"><small> The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.<a href="/motm/motm-about">More</a></small> </div> </div> </div> </div> <script> $('#iframe').load(function () { $(this).height($(this).contents().find('body').height() + 30); }); </script> </div> <div id="footer_main" class="hidden-print"> <div class="container"> <div class="row"> <div class="col-sm-12 col-md-7"> <p><strong>About PDB-101</strong></p> <p>Researchers around the globe make 3D structures freely available from the Protein Data Bank (PDB) archive. PDB-101 training materials help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. Outreach content demonstrate how PDB data impact fundamental biology, biomedicine, bioengineering/biotechnology, and energy sciences in 3D for a diverse and multidisciplinary user community. Education Materials provide lessons and activities for teaching and learning.</p> <p>PDB-101 is developed by the <a href="https://rcsb.org" target="_blank">RCSB PDB</a>.</p> </div> <div class="col-sm-12 col-md-5 text-center"> <p>RCSB PDB (<a href="http://nar.oxfordjournals.org/content/28/1/235.abstract" target="blank">citation</a>) is hosted by</p><img src="//cdn.rcsb.org/pdb101/common/images/Logo_Rutgers-2024.png" alt="Rutgers University logo" usemap="#rutgers-map" height="32" style="padding:0px 10px; border-right: 1px solid #000000;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSD-SDSC.png" alt="University of California San Diego/San Diego Supercomputer Center logos" usemap="#UCSD-SDSC-map" height="26" style="padding: 0px 10px; border-right: 1px solid #000000;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSF.png" alt="Univesity of California San Franciscologo" usemap="#UCSF-map" height="26" style="padding-left: 10px;"><map name="rutgers-map"> <area shape="rect" coords="0,0,115,26" href="http://www.rutgers.edu/" alt="Rutgers" target="_blank"></map><map name="UCSD-SDSC-map"> <area shape="rect" coords="0,0,150,26" href="http://ucsd.edu/" alt="UCSD" target="_blank"> <area shape="rect" coords="151,0,255,26" href="http://www.sdsc.edu/" alt="SDSC" target="_blank"></map><map name="UCSF-map"> <area shape="rect" coords="0,0,64,26" href="http://www.ucsf.edu/" alt="UCSF" target="_blank"></map><br><br> <p>RCSB PDB is a member of <span id='pdbmembers_footer'><a href='http://www.wwpdb.org/' target='_blank'><img src='//cdn.rcsb.org/pdb101/common/images/Logo_wwpdb.png' width='70'></a><span class='pipe'></span><a href='http://www.emdatabank.org/' target='_blank'><img src='https://cdn.rcsb.org/pdb101/common/images/EMDataResourcelogo.png' width='100'></a></p> </div> </div> </div> </div> <div id="footer_grant" class="hidden-print"> <div class="container"> <div class="row"> <p>RCSB PDB Core Operations are funded by the <a href="http://www.nsf.gov/" target="_blank">U.S. National Science Foundation</a> (DBI-2321666), the <a href="http://science.energy.gov/" target="_blank">US Department of Energy</a> (DE-SC0019749), and the <a href="http://www.cancer.gov/" target="_blank">National Cancer Institute</a>, <a href="http://www.niaid.nih.gov/" target="_blank">National Institute of Allergy and Infectious Diseases</a>, and <a href="http://www.nigms.nih.gov/" target="_blank">National Institute of General Medical Sciences</a> of the <a href="http://www.nih.gov/" target="_blank">National Institutes of Health</a> under grant R01GM157729.</p> </div> </div> </div> <div id="jira-fdbck"></div><script> //Google Analytics tracking code {/* (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-71059016-1', 'auto'); ga('send', 'pageview'); */} </script> </div> </body> </html>

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PDB-101: Molecule of the Month: Pyruvate Dehydrogenase Complex