5K3F

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His280Asn/Fluoroacetate - Cocrystallized - Single Protomer Reacted with Ligand

Summary for 5K3F

• Entry DOI: 10.2210/pdb5k3f/pdb
• Related: 5K3A 5K3B 5K3C 5K3D 5K3E
• Descriptor: Fluoroacetate dehalogenase, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: homodimer, hydrolase, dehalogenase
• Biological source: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009); More
• Total number of polymer chains: 2
• Total formula weight: 68192.72

Authors

Mehrabi, P.,Kim, T.H.,Prosser, S.R.,Pai, E.F. (deposition date: 2016-05-19, release date: 2017-02-01, Last modification date: 2023-11-15)

Primary citation

Kim, T.H.,Mehrabi, P.,Ren, Z.,Sljoka, A.,Ing, C.,Bezginov, A.,Ye, L.,Pomes, R.,Prosser, R.S.,Pai, E.F.
The role of dimer asymmetry and protomer dynamics in enzyme catalysis.
Science, 355:-, 2017

PubMed Abstract: 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.

PubMed: 28104837
DOI: 10.1126/science.aag2355

Experimental method

X-RAY DIFFRACTION (1.54 Å)