5T02

Structural characterisation of mutant Asp39Ala of thioesterase (NmACH) from Neisseria meningitidis

Summary for 5T02

• Entry DOI: 10.2210/pdb5t02/pdb
• Related: 5SZU 5SZV 5SZY 5SZZ
• Descriptor: Acyl-CoA hydrolase, GUANOSINE-5'-DIPHOSPHATE, COENZYME A, ... (4 entities in total)
• Functional Keywords: thioesterase, nisseria meningitidis, 4hbt, hydrolase, acyl-coa thioesterase, coenzyme a, gdp
• Biological source: Neisseria meningitidis
• Total number of polymer chains: 6
• Total formula weight: 115288.79

Authors

Khandokar, Y.B.,Srivastava, P.,Forwood, J.K. (deposition date: 2016-08-15, release date: 2016-09-07, Last modification date: 2023-10-04)

Primary citation

Khandokar, Y.B.,Srivastava, P.,Cowieson, N.,Sarker, S.,Aragao, D.,Das, S.,Smith, K.M.,Raidal, S.R.,Forwood, J.K.
Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.
J. Biol. Chem., 292:20461-20471, 2017

PubMed Abstract: Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn and Asp as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.

PubMed: 28972175
DOI: 10.1074/jbc.M117.800227

Experimental method

X-RAY DIFFRACTION (2.8 Å)