PXD006234

PXD006234 is an original dataset announced via ProteomeXchange.

Title	Hydrogen exchange soybean lipoxygenase
Description	Defining specific pathways for efficient heat transfer from protein-solvent interfaces to their active sites represents one of the compelling and timely challenges in our quest for a physical description of the origins of enzyme catalysis. Enzymatic hydrogen tunneling reactions constitute excellent systems in which to validate experimental approaches to this important question, given the inherent temperature independence of quantum mechanical wave function overlap. Herein, we present the application of hydrogen deuterium exchange coupled to mass spectrometry toward the spatial resolution of protein motions that can be related to the chemical reaction within an enzyme active site. Employing the proton-coupled electron transfer reaction of soybean lipoxygenase as proof of principle, we first corroborate the impact of active site mutation on increased local flexibility and second, uncover a solvent-exposed loop, 15-34 Å from the reactive ferric center whose temperature-dependent motions are demonstrated to mirror the enthalpic barrier for catalytic C-H bond cleavage. A network that connects this surface loop to the active site is structurally identified and supported by changes in kinetic parameters that result from site-specific mutations.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:33:20.923.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Adam Offenbacher
SpeciesList	scientific name: Glycine max; NCBI TaxID: 3847;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-03 01:28:04	ID requested
1	2022-02-22 03:49:21	announced
⏵ 2	2024-10-22 05:33:29	announced	2024-10-22: Updated project metadata.

10.1021/acscentsci.7b00142;

Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP, Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling. ACS Cent Sci, 3(6):570-579(2017) [pubmed]

curator keyword: Biological

submitter keyword: HDXMS, soybean lipoxygenase

Judith P. Klinman
contact affiliation	University of California, Berkeley
contact email	klinman@berkeley.edu
lab head
Adam Offenbacher
contact affiliation	University of California, Berkeley
contact email	offenbacher@berkeley.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD006234

PRIDE project URI

• PRIDE
  1. PXD006234
     1. Label: PRIDE project
     2. Name: Hydrogen exchange soybean lipoxygenase