Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate
- PMID: 27933791
- DOI: 10.1021/acs.biochem.6b00889
Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate
Abstract
o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.
Similar articles
-
Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode.J Biol Chem. 2017 Jul 21;292(29):12296-12310. doi: 10.1074/jbc.M117.790410. Epub 2017 May 30. J Biol Chem. 2017. PMID: 28559280 Free PMC article.
-
Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase.J Biol Chem. 2015 Sep 25;290(39):23971-83. doi: 10.1074/jbc.M115.676304. Epub 2015 Aug 14. J Biol Chem. 2015. PMID: 26276389 Free PMC article.
-
Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.Biochemistry. 2008 Nov 25;47(47):12434-47. doi: 10.1021/bi801311d. Biochemistry. 2008. PMID: 18973344 Free PMC article.
-
Investigating the Role of Class I Adenylate-Forming Enzymes in Natural Product Biosynthesis.ACS Chem Biol. 2020 Jan 17;15(1):17-27. doi: 10.1021/acschembio.9b00865. Epub 2019 Dec 20. ACS Chem Biol. 2020. PMID: 31815417 Review.
-
Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase.ACS Chem Biol. 2009 Oct 16;4(10):811-27. doi: 10.1021/cb900156h. ACS Chem Biol. 2009. PMID: 19610673 Free PMC article. Review.
Cited by
-
Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE.Biochemistry. 2019 Apr 9;58(14):1918-1930. doi: 10.1021/acs.biochem.9b00003. Epub 2019 Mar 26. Biochemistry. 2019. PMID: 30912442 Free PMC article.
-
Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.Genes (Basel). 2021 Jun 24;12(7):963. doi: 10.3390/genes12070963. Genes (Basel). 2021. PMID: 34202810 Free PMC article.
-
Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode.J Biol Chem. 2017 Jul 21;292(29):12296-12310. doi: 10.1074/jbc.M117.790410. Epub 2017 May 30. J Biol Chem. 2017. PMID: 28559280 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases