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| | ==Crystal structure of Menaquinol:fumarate oxidoreductase in complex with glutarate== | | ==Crystal structure of Menaquinol:fumarate oxidoreductase in complex with glutarate== |
| - | <StructureSection load='3p4r' size='340' side='right' caption='[[3p4r]], [[Resolution|resolution]] 3.05Å' scene=''> | + | <StructureSection load='3p4r' size='340' side='right'caption='[[3p4r]], [[Resolution|resolution]] 3.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3p4r]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Eaec_042 Eaec 042] and [http://en.wikipedia.org/wiki/Ecocb Ecocb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P4R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3p4r]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_042 Escherichia coli 042] and [https://en.wikipedia.org/wiki/Escherichia_coli_O55:H7_str._CB9615 Escherichia coli O55:H7 str. CB9615]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P4R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 3.05Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3p4q|3p4q]], [[3p4p|3p4p]], [[3p4s|3p4s]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EC042_4630, frdA, SDY_4398 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216592 EAEC 042]), frdB, EC042_4629 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216592 EAEC 042]), frdC, G2583_4981 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=701177 ECOCB]), frdD, EC042_4627 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216592 EAEC 042])</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=3p4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p4r OCA], [https://pdbe.org/3p4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p4r RCSB], [https://www.ebi.ac.uk/pdbsum/3p4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p4r 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/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] </span></td></tr>
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| - | <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=3p4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p4r OCA], [http://pdbe.org/3p4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3p4r RCSB], [http://www.ebi.ac.uk/pdbsum/3p4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3p4r ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/D3GV53_ECO44 D3GV53_ECO44]] Seems to be involved in the anchoring of the catalytic components of the fumarate reductase complex to the cytoplasmic membrane (By similarity).[HAMAP-Rule:MF_00709][SAAS:SAAS003418_004_011403] [[http://www.uniprot.org/uniprot/D3QL74_ECOCB D3QL74_ECOCB]] Seems to be involved in the anchoring of the catalytic components of the fumarate reductase complex to the cytoplasmic membrane (By similarity).[HAMAP-Rule:MF_00708][SAAS:SAAS003510_004_011403] | + | [https://www.uniprot.org/uniprot/FRDB_ECOLI FRDB_ECOLI] Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth. |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Complex II superfamily members catalyze the kinetically difficult interconversion of succinate and fumarate. Due to the relative simplicity of complex II substrates and their similarity to other biologically abundant small molecules, substrate specificity presents a challenge in this system. In order to identify determinants for on-pathway catalysis, off-pathway catalysis, and enzyme inhibition, crystal structures of Escherichia coli menaquinol:fumarate reductase (QFR), a complex II superfamily member, were determined bound to the substrate, fumarate, and the inhibitors oxaloacetate, glutarate, and 3-nitropropionate. Optical difference spectroscopy and computational modeling support a model where QFR twists the dicarboxylate, activating it for catalysis. Orientation of the C2-C3 double bond of activated fumarate parallel to the C(4a)-N5 bond of FAD allows orbital overlap between the substrate and the cofactor, priming the substrate for nucleophilic attack. Off-pathway catalysis, such as the conversion of malate to oxaloacetate or the activation of the toxin 3-nitropropionate may occur when inhibitors bind with a similarly activated bond in the same position. Conversely, inhibitors that do not orient an activatable bond in this manner, such as glutarate and citrate, are excluded from catalysis and act as inhibitors of substrate binding. These results support a model where electronic interactions via geometric constraint and orbital steering underlie catalysis by QFR.
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| - | Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase.,Tomasiak TM, Archuleta TL, Andrell J, Lunz-Chavez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, McLashina E, Cecchini G, Iverson TM J Biol Chem. 2010 Nov 23. PMID:21098488<ref>PMID:21098488</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3p4r" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Eaec 042]] | + | [[Category: Escherichia coli 042]] |
| - | [[Category: Ecocb]] | + | [[Category: Escherichia coli O55:H7 str. CB9615]] |
| - | [[Category: Succinate dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Andrell, J]] | + | [[Category: Andrell J]] |
| - | [[Category: Archuleta, T L]] | + | [[Category: Archuleta TL]] |
| - | [[Category: Cecchini, G]] | + | [[Category: Cecchini G]] |
| - | [[Category: Davis, T A]] | + | [[Category: Davis TA]] |
| - | [[Category: Ham, A J]] | + | [[Category: Ham AJ]] |
| - | [[Category: Iverson, T M]] | + | [[Category: Iverson TM]] |
| - | [[Category: Johnston, J N]] | + | [[Category: Johnston JN]] |
| - | [[Category: Luna-Chavez, C]] | + | [[Category: Luna-Chavez C]] |
| - | [[Category: Maklashina, E]] | + | [[Category: Maklashina E]] |
| - | [[Category: McDonald, W H]] | + | [[Category: McDonald WH]] |
| - | [[Category: Sarwar, M]] | + | [[Category: Sarwar M]] |
| - | [[Category: Stern, H A]] | + | [[Category: Stern HA]] |
| - | [[Category: Tomasiak, T M]] | + | [[Category: Tomasiak TM]] |
| - | [[Category: Yankowskaya, V]] | + | [[Category: Yankowskaya V]] |
| - | [[Category: Oxidoreductase]]
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