6es9 | pdb_00006es9

Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide

spinqualitylabelsall models 6es9, resolution 1.37Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6es9 is a 2 chain structure with sequence from Paracoccus denitrificans PD1222. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: COA, FAD, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [A1B5Y0_PARDP] Publication Abstract from PubMed (2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to alpha,beta-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 A. The enzyme forms a homodimer of two 60 kDa subunits. Compared to other ACDs, MCD contains a ~170 residue long N-terminal extension that structurally mimics a dimer-dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an alpha-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved towards preventing the unspecific oxidation of succinyl-CoA, a close structural homolog of (2S)-methylsuccinyl-CoA, and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD towards succinyl-CoA through active site mutagenesis. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase: an unusual member of the acyl-CoA dehydrogenase family.,Schwander T, McLean R, Zarzycki J, Erb TJ J Biol Chem. 2017 Dec 22. pii: RA117.000764. doi: 10.1074/jbc.RA117.000764. PMID:29275330 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Acyl-CoA dehydrogenase 3D structures

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