6MLK image
Entry Detail
PDB ID:
6MLK
Keywords:
Title:
Structure of Thioesterase from DEBS with a thioesterase-specific antibody
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2018-09-27
Release Date:
2018-10-17
Method Details:
Experimental Method:
Resolution:
2.45 Å
R-Value Free:
0.23
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
Chain IDs:A
Chain Length:300
Number of Molecules:1
Biological Source:Saccharopolyspora erythraea
Polymer Type:polypeptide(L)
Description:Heavy chain of Fab 3A6
Chain IDs:C (auth: H)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Light chain of Fab 3A6
Chain IDs:B (auth: L)
Chain Length:235
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Discovery and Characterization of a Thioesterase-Specific Monoclonal Antibody That Recognizes the 6-Deoxyerythronolide B Synthase.
Biochemistry 57 6201 6208 (2018)
PMID: 30289692 DOI: 10.1021/acs.biochem.8b00886

Abstact

Assembly line polyketide synthases (PKSs) are large multimodular enzymes responsible for the biosynthesis of diverse antibiotics in bacteria. Structural and mechanistic analysis of these megasynthases can benefit from the discovery of reagents that recognize individual domains or linkers in a site-specific manner. Monoclonal antibodies not only have proven themselves as premier tools in analogous applications but also have the added benefit of constraining the conformational flexibility of their targets in unpredictable but often useful ways. Here we have exploited a library based on the naïve human antibody repertoire to discover a Fab (3A6) that recognizes the terminal thioesterase (TE) domain of the 6-deoxyerythronolide B synthase with high specificity. Biochemical assays were used to verify that 3A6 binding does not inhibit enzyme turnover. The co-crystal structure of the TE-3A6 complex was determined at 2.45 Å resolution, resulting in atomic characterization of this protein-protein recognition mechanism. Fab binding had minimal effects on the structural integrity of the TE. In turn, these insights were used to interrogate via small-angle X-ray scattering the solution-phase conformation of 3A6 complexed to a catalytically competent PKS module and bimodule. Altogether, we have developed a high-affinity monoclonal antibody tool that recognizes the TE domain of the 6-deoxyerythronolide B synthase while maintaining its native function.

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