7SOI

Structure of I552A Soybean Lipoxygenase at 277K

Summary for 7SOI

• Entry DOI: 10.2210/pdb7soi/pdb
• Descriptor: Lipoxygenase, FE (III) ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: metal binding, lipid binding, oxidoreductase
• Biological source: Glycine max (Soybean, Glycine hispida)
• Total number of polymer chains: 2
• Total formula weight: 189094.84

Authors

Gee, C.L.,Offenbacher, A.R.,Hu, S. (deposition date: 2021-10-31, release date: 2022-11-09, Last modification date: 2023-10-25)

Primary citation

Zaragoza, J.P.T.,Offenbacher, A.R.,Hu, S.,Gee, C.L.,Firestein, Z.M.,Minnetian, N.,Deng, Z.,Fan, F.,Iavarone, A.T.,Klinman, J.P.
Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase.
Proc.Natl.Acad.Sci.USA, 120:e2211630120-e2211630120, 2023

PubMed Abstract: The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen-deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein-solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation () for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.

PubMed: 36867685
DOI: 10.1073/pnas.2211630120

Experimental method

X-RAY DIFFRACTION (2 Å)