6WH9 image
Entry Detail
PDB ID:
6WH9
Title:
Ketoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in complex with antibody fragment (Fab) 1D10
Biological Source:
PDB Version:
Deposition Date:
2020-04-07
Release Date:
2020-09-09
Method Details:
Experimental Method:
Resolution:
2.75 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:1D10 (Fab heavy chain)
Chain IDs:B (auth: E), D (auth: B), F (auth: H)
Chain Length:246
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:1D10 (Fab light chain)
Chain IDs:C (auth: F), E (auth: C), G (auth: I)
Chain Length:231
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:KR1
Chain IDs:A (auth: G), H (auth: D), I (auth: A)
Chain Length:485
Number of Molecules:3
Biological Source:Saccharopolyspora erythraea
Ligand Molecules
Primary Citation
Antibody Probes of Module 1 of the 6-Deoxyerythronolide B Synthase Reveal an Extended Conformation During Ketoreduction.
J.Am.Chem.Soc. 142 14933 14939 (2020)
PMID: 32786753 DOI: 10.1021/jacs.0c05133

Abstact

The 6-deoxyerythronolide B synthase (DEBS) is a prototypical assembly line polyketide synthase (PKS) that synthesizes the macrocyclic core of the antibiotic erythromycin. Each of its six multidomain modules presumably sample distinct conformations, as biosynthetic intermediates tethered to their acyl carrier proteins interact with multiple active sites during the courses of their catalytic cycles. The spatiotemporal details underlying these protein dynamics remain elusive. Here, we investigate one aspect of this conformational flexibility using two domain-specific monoclonal antibody fragments (Fabs) isolated from a very large naïve human antibody library. Both Fabs, designated 1D10 and 2G10, were bound specifically and with high affinity to the ketoreductase domain of DEBS module 1 (KR1). Comparative kinetic analysis of stand-alone KR1 as well as a truncated bimodular derivative of DEBS revealed that 1D10 inhibited KR1 activity whereas 2G10 did not. Co-crystal structures of each KR1-Fab complex provided a mechanistic rationale for this difference. A hybrid PKS module harboring KR1 was engineered, whose individual catalytic domains have been crystallographically characterized at high resolution. Size exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS) of this hybrid module bound to 1D10 provided further support for the catalytic relevance of the "extended" model of a PKS module. Our findings reinforce the power of monoclonal antibodies as tools to interrogate structure-function relationships of assembly line PKSs.

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Primary Citation of related structures