Crystal Structures of Malonyl-Coenzyme A Decarboxylase Provide Insights into Its Catalytic Mechanism and Disease-Causing Mutations

Froese, D. Sean; Forouhar, F.; Tran, Timothy H.; Vollmar, M.; Kim, Yi Seul; Lew, Scott; Neely, H.; Seetharaman, J.; Shen, Yang; Xiao, Rong; Acton, Thomas; Everett, J.K.; Cannone, Giuseppe; Puranik, Sriharsha; Savitsky, P.; Krojer, T.; Pilka, E.S.; Kiyani, W.; Lee, Wen‐Hwa; Marsden, Brian D.; Delft, Frank von; Allerston, C.K.; Spagnolo, Laura; Gileadi, O.; Montelione, Gaetano T.; Oppermann, U.; Yue, Wyatt W.; Tong, Liang

doi:10.1016/j.str.2013.05.001

Cited by 16 publications

(25 citation statements)

References 69 publications

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“…The k cat of this activity is 14-fold lower and the k cat / K m 38-fold lower than those of human MCD ( k cat = 33 s −1 and K m = 38 μM) 7 . Therefore, the MCD activity of MdcD–MdcE appears to be substantially weaker than a canonical MCD enzyme.…”

Section: Discussionmentioning

confidence: 68%

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer

et al. 2017

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Pseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD–MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Here we report the crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer, as well as biochemical and functional studies based on the structural information. We observe a malonate molecule in the active site of MdcA and we also determine the structure of malonate decarboxylase with CoA in the active site of MdcD–MdcE. Both structures provide molecular insights into malonate decarboxylase catalysis. Mutations in the hetero-tetramer interface can abolish holoenzyme formation. Mutations in the hetero-tetramer interface and the active sites can abolish Pseudomonas aeruginosa growth in a defined medium with malonate as the sole carbon source.

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Section: Discussionmentioning

confidence: 68%

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer

et al. 2017

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“…Structures of the wild-type and mutant metabolic enzymes determined at atomic resolution (i.e. with the details to resolve individual amino acid residues) prove useful in ascertaining the structural and molecular principles for the amino acid substitution in the local environment, as well as detecting mutation trends and hotspot regions on the protein polypeptide as a whole (Froese et al 2013; Shafqat et al 2013; Riemersma et al 2015). …”

Section: An Integrated (Structural Biochemical Computational) Appromentioning

confidence: 99%

From structural biology to designing therapy for inborn errors of metabolism

Yue

2016

J of Inher Metab Disea

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At the SSIEM Symposium in Istanbul 2010, I presented an overview of protein structural approaches in the study of inborn errors of metabolism (Yue and Oppermann 2011). Five years on, the field is going strong with new protein structures, uncovered catalytic functions and novel chemical matters for metabolic enzymes, setting the stage for the next generation of drug discovery. This article aims to update on recent advances and lessons learnt on inborn errors of metabolism via the protein-centric approach, citing examples of work from my group, collaborators and co-workers that cover diverse pathways of transsulfuration, cobalamin and glycogen metabolism. Taking into consideration that many inborn errors of metabolism result in the loss of enzyme function, this presentation aims to outline three key principles that guide the design of small molecule therapy in this technically challenging field: (1) integrating structural, biochemical and cell-based data to evaluate the wide spectrum of mutation-driven enzyme defects in stability, catalysis and protein-protein interaction; (2) studying multi-domain proteins and multi-protein complexes as examples from nature, to learn how enzymes are activated by small molecules; (3) surveying different regions of the enzyme, away from its active site, that can be targeted for the design of allosteric activators and inhibitors.

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“…The monomer of MCD has an N-terminal helical domain for oligomerization and a C-terminal domain for catalysis, and the active site of MCD is located in a prominent groove clustered with evolutionarily conserved residues (Fig. 5a) (Aparicio et al 2013;Froese et al 2013). Through inter-subunit disulfide bonds, Cys-206-Cys-206 and Cys-243-Cys-243 (Fig.…”

Section: Structural Implication Of Hmcd Phosphorylationmentioning

confidence: 99%

Phosphorylation of Ser-204 and Tyr-405 in human malonyl-CoA decarboxylase expressed in silkworm Bombyx mori regulates catalytic decarboxylase activity

Hwang

Makishima

Suzuki

et al. 2015

Appl Microbiol Biotechnol

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Decarboxylation of malonyl-CoA to acetyl-CoA by malonyl-CoA decarboxylase (MCD; EC 4.1.1.9) is a vital catalytic reaction of lipid metabolism. While it is established that phosphorylation of MCD modulates the enzymatic activity, the specific phosphorylation sites associated with the catalytic function have not been documented due to lack of sufficient production of MCD with proper post-translational modifications. Here, we used the silkworm-based Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid system to express human MCD (hMCD) and mapped phosphorylation effects on enzymatic function. Purified MCD from silkworm displayed post-translational phosphorylation and demonstrated coherent enzymatic activity with high yield (-200 μg/silkworm). Point mutations in putative phosphorylation sites, Ser-204 or Tyr-405 of hMCD, identified by bioinformatics and proteomics analyses reduced the catalytic activity, underscoring the functional significance of phosphorylation in modulating decarboxylase-based catalysis. Identified phosphorylated residues are distinct from the decarboxylation catalytic site, implicating a phosphorylation-induced global conformational change of MCD as responsible in altering catalytic function. We conclude that phosphorylation of Ser-204 and Tyr-405 regulates the decarboxylase function of hMCD leveraging the silkworm-based BmNPV bacmid expression system that offers a fail-safe eukaryotic production platform implementing proper post-translational modification such as phosphorylation.

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Crystal Structures of Malonyl-Coenzyme A Decarboxylase Provide Insights into Its Catalytic Mechanism and Disease-Causing Mutations

Cited by 16 publications

References 69 publications

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer

From structural biology to designing therapy for inborn errors of metabolism

Phosphorylation of Ser-204 and Tyr-405 in human malonyl-CoA decarboxylase expressed in silkworm Bombyx mori regulates catalytic decarboxylase activity

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