Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase fromMycobacterium smegmatis
- 27 November 2015
- journal article
- research article
- Published by International Union of Crystallography (IUCr) in Acta crystallographica. Section D, Structural biology
- Vol. 71 (12), 2479-2493
- https://doi.org/10.1107/s1399004715019331
Abstract
Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) fromMycobacterium smegmatisin apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domainviaflexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1–covering loop–Lα2 region, together with the Nβ2–Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.Keywords
This publication has 35 references indexed in Scilit:
- Overview of theCCP4 suite and current developmentsActa crystallographica. Section D, Structural biology, 2011
- Features and development of CootActa crystallographica. Section D, Structural biology, 2010
- Iterative model building, structure refinement and density modification with thePHENIX AutoBuildwizardActa crystallographica. Section D, Structural biology, 2007
- Inference of Macromolecular Assemblies from Crystalline StateJournal of Molecular Biology, 2007
- Phasercrystallographic softwareJournal of Applied Crystallography, 2007
- Automated ligand fitting by core-fragment fitting and extension into densityActa crystallographica. Section D, Structural biology, 2006
- Scaling and assessment of data qualityActa crystallographica. Section D, Structural biology, 2005
- [20] Processing of X-ray diffraction data collected in oscillation modeMethods in Enzymology, 1997
- A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye bindingAnalytical Biochemistry, 1976
- Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4Nature, 1970