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| | ==Structure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA complex== | | ==Structure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA complex== |
| - | <StructureSection load='3mpi' size='340' side='right' caption='[[3mpi]], [[Resolution|resolution]] 2.05Å' scene=''> | + | <StructureSection load='3mpi' size='340' side='right'caption='[[3mpi]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3mpi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33890 Atcc 33890]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MPI FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GRA:GLUTARYL-COENZYME+A'>GRA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mpj|3mpj]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">acd, gi228015642 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=897 ATCC 33890])</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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutaryl-CoA_dehydrogenase_(ETF) Glutaryl-CoA dehydrogenase (ETF)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.6 1.3.8.6] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3mpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mpi OCA], [http://pdbe.org/3mpi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mpi RCSB], [http://www.ebi.ac.uk/pdbsum/3mpi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mpi ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ACD_DESML ACD_DESML]] Catalyzes the dehydrogenation of Glutaryl-CoA to glutaconyl-CoA.<ref>PMID:19395484</ref> | + | [https://www.uniprot.org/uniprot/ACD_DESML ACD_DESML] Catalyzes the dehydrogenation of Glutaryl-CoA to glutaconyl-CoA.<ref>PMID:19395484</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| | + | *[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]] |
| | *[[Glutaryl-CoA dehydrogenase|Glutaryl-CoA dehydrogenase]] | | *[[Glutaryl-CoA dehydrogenase|Glutaryl-CoA dehydrogenase]] |
| | == References == | | == References == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 33890]] | + | [[Category: Desulfococcus multivorans]] |
| - | [[Category: Boll, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Ermler, U]] | + | [[Category: Boll M]] |
| - | [[Category: Warkentin, E]] | + | [[Category: Ermler U]] |
| - | [[Category: Wischgoll, S]] | + | [[Category: Warkentin E]] |
| - | [[Category: Alpha-beta fold]]
| + | [[Category: Wischgoll S]] |
| - | [[Category: Dehydrogenase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
ACD_DESML Catalyzes the dehydrogenation of Glutaryl-CoA to glutaconyl-CoA.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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 --> 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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wischgoll S, Taubert M, Peters F, Jehmlich N, von Bergen M, Boll M. Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria. J Bacteriol. 2009 Jul;191(13):4401-9. doi: 10.1128/JB.00205-09. Epub 2009 Apr 24. PMID:19395484 doi:http://dx.doi.org/10.1128/JB.00205-09
- ↑ Wischgoll S, Demmer U, Warkentin E, Gunther R, Boll M, Ermler U. Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases. Biochemistry. 2010 Jun 29;49(25):5350-7. PMID:20486657 doi:10.1021/bi100317m
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