View source for 3mpi


==Structure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA complex==
<StructureSection load='3mpi' size='340' side='right'caption='[[3mpi]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3mpi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfococcus_multivorans Desulfococcus multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MPI FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GRA:GLUTARYL-COENZYME+A'>GRA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mpi OCA], [https://pdbe.org/3mpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mpi RCSB], [https://www.ebi.ac.uk/pdbsum/3mpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mpi ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ACD_DESML ACD_DESML] Catalyzes the dehydrogenation of Glutaryl-CoA to glutaconyl-CoA.<ref>PMID:19395484</ref> 
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mp/3mpi_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3mpi ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glutaryl-coenzyme A dehydrogenases (GDHs) involved in amino acid degradation were thought to catalyze both the dehydrogenation and decarboxylation of glutaryl-coenzyme A to crotonyl-coenzyme A and CO(2). Recently, a structurally related but nondecarboxylating, glutaconyl-coenzyme A-forming GDH was characterized in the obligately anaerobic bacteria Desulfococcus multivorans (GDH(Des)) which conserves the free energy of decarboxylation by a Na(+)-pumping glutaconyl-coenzyme A decarboxylase. To understand the distinct catalytic behavior of the two GDH types on an atomic basis, we determined the crystal structure of GDH(Des) with and without glutaconyl-coenzyme A bound at 2.05 and 2.1 A resolution, respectively. The decarboxylating and nondecarboxylating capabilities are provided by complex structural changes around the glutaconyl carboxylate group, the key factor being a Tyr --&gt; Val exchange strictly conserved between the two GDH types. As a result, the interaction between the glutaconyl carboxylate and the guanidinium group of a conserved arginine is stronger in GDH(Des) (short and planar bidentate hydrogen bond) than in the decarboxylating human GDH (longer and monodentate hydrogen bond), which is corroborated by molecular dynamics studies. The identified structural changes prevent decarboxylation (i) by strengthening the C4-C5 bond of glutaconyl-coenzyme A, (ii) by reducing the leaving group potential of CO(2), and (iii) by increasing the distance between the C4 atom (negatively charged in the dienolate transition state) and the adjacent glutamic acid.

Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases.,Wischgoll S, Demmer U, Warkentin E, Gunther R, Boll M, Ermler U Biochemistry. 2010 Jun 29;49(25):5350-7. PMID:20486657<ref>PMID:20486657</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3mpi" style="background-color:#fffaf0;"></div>

==See Also==
*[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]]
*[[Glutaryl-CoA dehydrogenase|Glutaryl-CoA dehydrogenase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Desulfococcus multivorans]]
[[Category: Large Structures]]
[[Category: Boll M]]
[[Category: Ermler U]]
[[Category: Warkentin E]]
[[Category: Wischgoll S]]