Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase.
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.
From the Department of Chemistry and State Key Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
Yaozong
Y
Chen
From the Department of Chemistry and State Key Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
Yueru
Y
Sun
From the Department of Chemistry and State Key Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
Haigang
H
Song
From the Department of Chemistry and State Key Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China chguo@ust.hk.
Zhihong
Z
Guo
D000255:Adenosine Triphosphate / Q000737:chemistry*; D001412:Bacillus subtilis / Q000201:enzymology* / Q000235:genetics; D002384:Catalysis; D020134:Catalytic Domain; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D013379:Substrate Specificity; D013389:Succinate-CoA Ligases / Q000737:chemistry* / Q000235:genetics
D000255:Adenosine Triphosphate; D013389:Succinate-CoA Ligases; C022693:O-succinylbenzoate - CoA ligase
ATP; adenylate forming enzyme; crystal structure; domain alteration; enzyme mechanism; open-closed conformational change; protein conformation; vitamin K