5GTD
o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis in Complex with the Acyl-adenylate Intermediate OSB-AMP
Summary for 5GTD
| Entry DOI | 10.2210/pdb5gtd/pdb |
| Descriptor | 2-succinylbenzoate--CoA ligase, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... (8 entities in total) |
| Functional Keywords | adenylate-forming enzyme, adenylate intermdiate, osbamp, in-line backside nucleophilic substitution, strained conformation, ligase |
| Biological source | Bacillus subtilis (strain 168) |
| Total number of polymer chains | 2 |
| Total formula weight | 112018.39 |
| Authors | |
| Primary citation | Chen, Y.,Jiang, Y.,Guo, Z. Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate Biochemistry, 55:6685-6695, 2016 Cited by PubMed 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. PubMed: 27933791DOI: 10.1021/acs.biochem.6b00889 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.69 Å) |
Structure validation
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