8cej: Difference between revisions
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<table><tr><td colspan='2'>[[8cej]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_kluyveri Clostridium kluyveri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CEJ FirstGlance]. <br> | <table><tr><td colspan='2'>[[8cej]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_kluyveri Clostridium kluyveri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CEJ 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]] 2.1Å</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]] 2.1Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MEZ:(2E)-2-METHYLBUT-2-ENEDIOIC+ACID'>MEZ</scene>, <scene name='pdbligand=OA9: | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MEZ:(2E)-2-METHYLBUT-2-ENEDIOIC+ACID'>MEZ</scene>, <scene name='pdbligand=OA9:(~{E})-4-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-methyl-4-oxidanylidene-but-2-enoic+acid'>OA9</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=8cej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8cej OCA], [https://pdbe.org/8cej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8cej RCSB], [https://www.ebi.ac.uk/pdbsum/8cej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8cej 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=8cej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8cej OCA], [https://pdbe.org/8cej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8cej RCSB], [https://www.ebi.ac.uk/pdbsum/8cej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8cej ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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Succinyl-CoA reductase (SucD) is an acylating aldehyde reductase that catalyzes the NADPH-dependent reduction of succinyl-CoA to succinic semialdehyde. The reaction sequence from succinate to crotonyl-CoA is of particular interest for several new-to-nature CO(2)-fixation pathways, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, in which SucD plays a key role. However, pathways like the CETCH cycle feature several CoA-ester intermediates, which could be potentially side substrates for this enzyme. Here, we show that the side reaction for most CETCH cycle metabolites is relatively small (<2%) with the exception of mesaconyl-C1-CoA (16%), which represents a competing substrate in this pathway. We addressed this promiscuity by solving the crystal structure of a SucD of Clostridium kluyveri in complex with NADP(+) and mesaconyl-C1-CoA. We further identified two residues (Lys70 and Ser243) that coordinate mesaconyl-C1-CoA at the active site. We targeted those residues with site-directed mutagenesis to improve succinyl-CoA over mesaconyl-C1-CoA reduction. The best resulting SucD variant, K70R, showed a strongly reduced side activity for mesaconyl-C1-CoA, but the substitution also reduced the specific activity for succinyl-CoA by a factor of 10. Transferring the same mutations into a SucD homologue from Clostridium difficile similarly decreases the side reaction of this enzyme for mesaconyl-C1-CoA from 12 to 2%, notably without changing the catalytic efficiency for succinyl-CoA. Overall, our structure-based engineering efforts provided a highly specific enzyme of interest for several applications in biocatalysis and synthetic biology. | Succinyl-CoA reductase (SucD) is an acylating aldehyde reductase that catalyzes the NADPH-dependent reduction of succinyl-CoA to succinic semialdehyde. The reaction sequence from succinate to crotonyl-CoA is of particular interest for several new-to-nature CO(2)-fixation pathways, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, in which SucD plays a key role. However, pathways like the CETCH cycle feature several CoA-ester intermediates, which could be potentially side substrates for this enzyme. Here, we show that the side reaction for most CETCH cycle metabolites is relatively small (<2%) with the exception of mesaconyl-C1-CoA (16%), which represents a competing substrate in this pathway. We addressed this promiscuity by solving the crystal structure of a SucD of Clostridium kluyveri in complex with NADP(+) and mesaconyl-C1-CoA. We further identified two residues (Lys70 and Ser243) that coordinate mesaconyl-C1-CoA at the active site. We targeted those residues with site-directed mutagenesis to improve succinyl-CoA over mesaconyl-C1-CoA reduction. The best resulting SucD variant, K70R, showed a strongly reduced side activity for mesaconyl-C1-CoA, but the substitution also reduced the specific activity for succinyl-CoA by a factor of 10. Transferring the same mutations into a SucD homologue from Clostridium difficile similarly decreases the side reaction of this enzyme for mesaconyl-C1-CoA from 12 to 2%, notably without changing the catalytic efficiency for succinyl-CoA. Overall, our structure-based engineering efforts provided a highly specific enzyme of interest for several applications in biocatalysis and synthetic biology. | ||
Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis.,Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ Biochemistry. 2023 | Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis.,Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ Biochemistry. 2023 Jun 6;62(11):1786-1793. doi: 10.1021/acs.biochem.3c00102. Epub , 2023 May 19. PMID:37207322<ref>PMID:37207322</ref> | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 8cej" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 8cej" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Succinate-semialdehyde dehydrogenase|Succinate-semialdehyde dehydrogenase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
Latest revision as of 10:06, 21 November 2024
Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with Mesaconyl-C1-CoASuccinyl-CoA Reductase from Clostridium kluyveri (SucD) with Mesaconyl-C1-CoA
Structural highlights
FunctionSUCD_CLOK5 Catalyzes the reduction of succinate semialdehyde to succinyl-CoA. The enzyme is specific for succinate semialdehyde and succinyl-CoA, and only shows low activity with palmitoyl-CoA. There is no activity with NAD(+) as cosubstrate. Publication Abstract from PubMedSuccinyl-CoA reductase (SucD) is an acylating aldehyde reductase that catalyzes the NADPH-dependent reduction of succinyl-CoA to succinic semialdehyde. The reaction sequence from succinate to crotonyl-CoA is of particular interest for several new-to-nature CO(2)-fixation pathways, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, in which SucD plays a key role. However, pathways like the CETCH cycle feature several CoA-ester intermediates, which could be potentially side substrates for this enzyme. Here, we show that the side reaction for most CETCH cycle metabolites is relatively small (<2%) with the exception of mesaconyl-C1-CoA (16%), which represents a competing substrate in this pathway. We addressed this promiscuity by solving the crystal structure of a SucD of Clostridium kluyveri in complex with NADP(+) and mesaconyl-C1-CoA. We further identified two residues (Lys70 and Ser243) that coordinate mesaconyl-C1-CoA at the active site. We targeted those residues with site-directed mutagenesis to improve succinyl-CoA over mesaconyl-C1-CoA reduction. The best resulting SucD variant, K70R, showed a strongly reduced side activity for mesaconyl-C1-CoA, but the substitution also reduced the specific activity for succinyl-CoA by a factor of 10. Transferring the same mutations into a SucD homologue from Clostridium difficile similarly decreases the side reaction of this enzyme for mesaconyl-C1-CoA from 12 to 2%, notably without changing the catalytic efficiency for succinyl-CoA. Overall, our structure-based engineering efforts provided a highly specific enzyme of interest for several applications in biocatalysis and synthetic biology. Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis.,Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ Biochemistry. 2023 Jun 6;62(11):1786-1793. doi: 10.1021/acs.biochem.3c00102. Epub , 2023 May 19. PMID:37207322[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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