5BUQ
Unliganded Form of O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Subtilis, Solved at 1.98 Angstroms
Summary for 5BUQ
| Entry DOI | 10.2210/pdb5buq/pdb |
| Related | 5BUR 5BUS |
| Descriptor | 2-succinylbenzoate--CoA ligase, ACETATE ION, CALCIUM ION, ... (4 entities in total) |
| Functional Keywords | apo, atp, amp, enzyme mechanism, protein conformation, vitamin k2, adenylate forming enzyme, domain alteration, open-closed conformational change, ligase |
| Biological source | Bacillus subtilis (strain 168) |
| Total number of polymer chains | 2 |
| Total formula weight | 110637.36 |
| Authors | |
| Primary citation | Chen, Y.,Sun, Y.,Song, H.,Guo, Z. Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase J.Biol.Chem., 290:23971-23983, 2015 Cited by PubMed Abstract: o-Succinylbenzoyl-CoA synthetase, or MenE, is an essential adenylate-forming enzyme targeted for development of novel antibiotics in the menaquinone biosynthesis. Using its crystal structures in a ligand-free form or in complex with nucleotides, a conserved pattern is identified in the interaction between ATP and adenylating enzymes, including acyl/aryl-CoA synthetases, adenylation domains of nonribosomal peptide synthetases, and luciferases. It involves tight gripping interactions of the phosphate-binding loop (P-loop) with the ATP triphosphate moiety and an open-closed conformational change to form a compact adenylation active site. In MenE catalysis, this ATP-enzyme interaction creates a new binding site for the carboxylate substrate, allowing revelation of the determinants of substrate specificities and in-line alignment of the two substrates for backside nucleophilic substitution reaction by molecular modeling. In addition, the ATP-enzyme interaction is suggested to play a crucial catalytic role by mutation of the P-loop residues hydrogen-bonded to ATP. Moreover, the ATP-enzyme interaction has also clarified the positioning and catalytic role of a conserved lysine residue in stabilization of the transition state. These findings provide new insights into the adenylation half-reaction in the domain alteration catalytic mechanism of the adenylate-forming enzymes. PubMed: 26276389DOI: 10.1074/jbc.M115.676304 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.98 Å) |
Structure validation
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