6KKH

Crystal structure of the oxalate bound malyl-CoA lyase from Roseiflexus castenholzii

Summary for 6KKH

• Entry DOI: 10.2210/pdb6kkh/pdb
• Descriptor: HpcH/HpaI aldolase, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, OXALATE ION, ... (5 entities in total)
• Functional Keywords: malyl-coa lyase, cite-like superfamily, roseiflexus castenholzii, conformational changes, lyase
• Biological source: Roseiflexus castenholzii (strain DSM 13941 / HLO8)
• Total number of polymer chains: 12
• Total formula weight: 460683.84

Authors

Tang, W.R.,Wang, Z.G.,Zhang, C.Y.,Wang, C. (deposition date: 2019-07-25, release date: 2019-09-04, Last modification date: 2023-11-22)

Primary citation

Tang, W.,Wang, Z.,Zhang, C.,Wang, C.,Min, Z.,Zhang, X.,Liu, D.,Shen, J.,Xu, X.
The C-terminal domain conformational switch revealed by the crystal structure of malyl-CoA lyase from Roseiflexus castenholzii.
Biochem.Biophys.Res.Commun., 518:72-79, 2019

PubMed Abstract: Malyl-coenzyme A lyase (MCL) is a carbon-carbon bond lyase that catalyzes the reversible cleavage of coenzyme A (CoA) thioesters in multiple carbon metabolic pathways. This enzyme contains a CitE-like TIM barrel and an additional C-terminal domain that undergoes conformational changes upon substrate binding. However, the structural basis underlying these conformational changes is elusive. Here, we report the crystal structure of MCL from the thermophilic photosynthetic bacterium Roseiflexus castenholzii (RfxMCL) in the apo- and oxalate-bound forms at resolutions of 2.50 and 2.65 Å, respectively. Molecular dynamics simulations and structural comparisons with MCLs from other species reveal the deflection of the C-terminal domain to close the adjacent active site pocket in the trimer and contribute active site residues for CoA coordination. The deflection angles of the C-terminal domain are not only related to the occupation but also the type of bound substrates in the adjacent active site pocket. Our work illustrates that a conformational switch of the C-terminal domain accompanies the substrate-binding of MCLs. The results provide a framework for further investigating the reaction mechanism and multifunctionality of MCLs in different carbon metabolic pathways.

PubMed: 31405562
DOI: 10.1016/j.bbrc.2019.08.010

Experimental method

X-RAY DIFFRACTION (2.64 Å)