5X8F

Ternary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with AMP and its product analogue OSB-NCoA at 1.76 angstrom

Summary for 5X8F

• Entry DOI: 10.2210/pdb5x8f/pdb
• Related: 5X8G
• Descriptor: 2-succinylbenzoate--CoA ligase, o-succinylbenzoyl-N-coenzyme A, ADENOSINE MONOPHOSPHATE, ... (8 entities in total)
• Functional Keywords: adenylate-forming enzyme, acyl-coa synthetase, thioester conformation, coa, pantetheine tunnel, adp binding subsite, domain alternation, large conformational change, inter-domain linker, ligase
• Biological source: Bacillus subtilis subsp. subtilis str. 168
• Total number of polymer chains: 4
• Total formula weight: 223682.85

Authors

Chen, Y.,Guo, Z. (deposition date: 2017-03-02, release date: 2017-06-07, Last modification date: 2023-11-22)

Primary citation

Chen, Y.,Li, T.L.,Lin, X.,Li, X.,Li, X.D.,Guo, Z.
Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode
J. Biol. Chem., 292:12296-12310, 2017

PubMed Abstract: -Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 Å resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5° during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family.

PubMed: 28559280
DOI: 10.1074/jbc.M117.790410

Experimental method

X-RAY DIFFRACTION (1.763 Å)