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8cej

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Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with Mesaconyl-C1-CoA

Structural highlights

8cej is a 4 chain structure with sequence from Clostridium kluyveri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUCD_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 PubMed

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 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.

References

↑ Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ. Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis. Biochemistry. 2023 May 19. PMID:37207322 doi:10.1021/acs.biochem.3c00102