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| | <StructureSection load='6pbr' size='340' side='right'caption='[[6pbr]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='6pbr' size='340' side='right'caption='[[6pbr]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6pbr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PBR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pbr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PBR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 3Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyllysine-residue_succinyltransferase Dihydrolipoyllysine-residue succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.61 2.3.1.61] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=6pbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbr OCA], [http://pdbe.org/6pbr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbr RCSB], [http://www.ebi.ac.uk/pdbsum/6pbr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbr ProSAT]</span></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=6pbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbr OCA], [https://pdbe.org/6pbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pbr RCSB], [https://www.ebi.ac.uk/pdbsum/6pbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbr ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0K4N9D8_ECOLX A0A0K4N9D8_ECOLX]] E2 component of the 2-oxoglutarate dehydrogenase (OGDH) complex which catalyzes the second step in the conversion of 2-oxoglutarate to succinyl-CoA and CO(2).[RuleBase:RU361138] | + | [https://www.uniprot.org/uniprot/ODO2_ECOLI ODO2_ECOLI] The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6pbr" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6pbr" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[2-oxoglutarate dehydrogenase 3D structures|2-oxoglutarate dehydrogenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dihydrolipoyllysine-residue succinyltransferase]] | |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Andi, B]] | + | [[Category: Andi B]] |
| - | [[Category: Fuchs, M R]] | + | [[Category: Fuchs MR]] |
| - | [[Category: Liu, Q]] | + | [[Category: Liu Q]] |
| - | [[Category: McSweeney, S]] | + | [[Category: McSweeney S]] |
| - | [[Category: Shi, W]] | + | [[Category: Shi W]] |
| - | [[Category: Soares, A S]] | + | [[Category: Soares AS]] |
| - | [[Category: 2-oxoglutarate dehydrogenase multienzyme complex]]
| + | |
| - | [[Category: Citric acid cycle]]
| + | |
| - | [[Category: Dihydrolipoamide succinyltransferase]]
| + | |
| - | [[Category: Krebs cycle]]
| + | |
| - | [[Category: Tca cycle]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
ODO2_ECOLI The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).
Publication Abstract from PubMed
The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 A) were obtained and diffracted to 3.0 A resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 A resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.
Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant.,Andi B, Soares AS, Shi W, Fuchs MR, McSweeney S, Liu Q Acta Crystallogr F Struct Biol Commun. 2019 Sep 1;75(Pt 9):616-624. doi:, 10.1107/S2053230X19011488. Epub 2019 Aug 29. PMID:31475929[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Andi B, Soares AS, Shi W, Fuchs MR, McSweeney S, Liu Q. Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. Acta Crystallogr F Struct Biol Commun. 2019 Sep 1;75(Pt 9):616-624. doi:, 10.1107/S2053230X19011488. Epub 2019 Aug 29. PMID:31475929 doi:http://dx.doi.org/10.1107/S2053230X19011488
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