5SWN image
Deposition Date 2016-08-08
Release Date 2017-02-01
Last Version Date 2023-10-04
Entry Detail
PDB ID:
5SWN
Keywords:
Title:
Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Fluoroacetate - Cocrystallized
Biological Source:
Method Details:
Experimental Method:
Resolution:
1.54 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Fluoroacetate dehalogenase
Gene (Uniprot):RPA1163
Mutations:D110N
Chain IDs:A, B
Chain Length:297
Number of Molecules:2
Biological Source:Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
Primary Citation
The role of dimer asymmetry and protomer dynamics in enzyme catalysis.
Science 355 ? ? (2017)
PMID: 28104837 DOI: 10.1126/science.aag2355

Abstact

Freeze-trapping x-ray crystallography, nuclear magnetic resonance, and computational techniques reveal the distribution of states and their interconversion rates along the reaction pathway of a bacterial homodimeric enzyme, fluoroacetate dehalogenase (FAcD). The crystal structure of apo-FAcD exhibits asymmetry around the dimer interface and cap domain, priming one protomer for substrate binding. This asymmetry is dynamically averaged through conformational exchange on a millisecond time scale. During catalysis, the protomer conformational exchange rate becomes enhanced, the empty protomer exhibits increased local disorder, and water egresses. Computational studies identify allosteric pathways between protomers. Water release and enhanced dynamics associated with catalysis compensate for entropic losses from substrate binding while facilitating sampling of the transition state. The studies provide insights into how substrate-coupled allosteric modulation of structure and dynamics facilitates catalysis in a homodimeric enzyme.

Legend

Protein

Chemical

Disease

Primary Citation of related structures