5D3K

Crystal structure of the thioesterase domain of deoxyerythronolide B synthase

Summary for 5D3K

• Entry DOI: 10.2210/pdb5d3k/pdb
• Related: 5D2R
• Descriptor: Erythronolide synthase, modules 5 and 6, PENTAETHYLENE GLYCOL, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: thioesterase domaine alpha / beta hydrolase fold deoxyerythronolide b synthase, hydrolase
• Biological source: Saccharopolyspora erythraea
• Total number of polymer chains: 1
• Total formula weight: 29377.94

Authors

Bergeret, F.,Argyropoulos, P.,Boddy, C.N.,Schmeing, T.M. (deposition date: 2015-08-06, release date: 2015-12-09, Last modification date: 2023-09-27)

Primary citation

Argyropoulos, P.,Bergeret, F.,Pardin, C.,Reimer, J.M.,Pinto, A.,Boddy, C.N.,Schmeing, T.M.
Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis.
Biochim.Biophys.Acta, 1860:486-497, 2015

PubMed Abstract: Type I polyketide synthases (PKSs) are giant multidomain proteins that synthesize many therapeutics and other natural products. The synthesis proceeds by a thiotemplate mechanism whereby intermediates are covalently attached to the PKS. The release of the final polyketide is catalyzed by the terminal thioesterase (TE) domain through hydrolysis, transesterification, or macrocyclization. The PKS 6-deoxyerythronolide B synthase (DEBS) produces the 14-membered macrolide core of the clinically important antibiotic erythromycin. The TE domain of DEBS (DEBS TE) has well-established, empirically-defined specificities for hydrolysis or macrocyclization of native and modified substrates. We present efforts towards understanding the structural basis for the specificity of the thioesterase reaction in DEBS TE using a set of novel diphenyl alkylphosphonates, which mimic substrates that are specifically cyclized or hydrolyzed by DEBS TE. We have determined structures of a new construct of DEBS TE alone at 1.7Å, and DEBS TE bound with a simple allylphosphonate at 2.1Å resolution. Other, more complex diphenyl alkylphosphonates inhibit DEBS TE, but we were unable to visualize these faithful cyclization analogs in complex with DEBS TE. This work represents a first step towards using DEBS TE complexed with sophisticated substrate analogs to decipher the specificity determinants in this important reaction.

PubMed: 26592346
DOI: 10.1016/j.bbagen.2015.11.007

Experimental method

X-RAY DIFFRACTION (1.7 Å)