5TQP

LIPOXYGENASE-1 (SOYBEAN) I553G MUTANT AT 300K

  • Classification: OXIDOREDUCTASE
  • Organism(s): Glycine max
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2016-10-24 Released: 2017-11-01 
  • Deposition Author(s): Poss, E.M., Fraser, J.S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Center for Research Resources 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.

Offenbacher, A.R.Hu, S.Poss, E.M.Carr, C.A.M.Scouras, A.D.Prigozhin, D.M.Iavarone, A.T.Palla, A.Alber, T.Fraser, J.S.Klinman, J.P.

(2017) ACS Cent Sci 3: 570-579

  • DOI: 10.1021/acscentsci.7b00142
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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 an enzyme's catalytic parameters. Employing the proton-coupled electron transfer reaction of soybean lipoxygenase as proof of principle, we first corroborate the impact of active site mutations 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.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, California 94720, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seed linoleate 13S-lipoxygenase-1
A, B
839Glycine maxMutation(s): 1 
Gene Names: LOX1.1 (LOX1)
EC: 1.13.11.12
Find proteins for P08170 (Glycine max)
Go to UniProtKB:  P08170
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.570α = 90.00
b = 92.868β = 93.41
c = 100.925γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM113432
National Institutes of Health/National Center for Research ResourcesUnited States1S10RR022393-01
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM025765

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references
  • Version 1.2: 2018-04-18
    Type: Data collection