5TQO

Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K

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

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Hu, S.Offenbacher, A.R.Thompson, E.M.Gee, C.L.Wilcoxen, J.Carr, C.A.M.Prigozhin, D.M.Yang, V.Alber, T.Britt, R.D.Fraser, J.S.Klinman, J.P.

(2019) J Am Chem Soc 141: 1555-1567

  • DOI: 10.1021/jacs.8b10992
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-indep ...

    Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-independence of its primary kinetic isotope effect, low catalytic efficiency, and elevated enthalpy of activation. To uncover the physical basis of these features, we herein apply three structural probes: hydrogen-deuterium exchange mass spectrometry, room-temperature X-ray crystallography and EPR spectroscopy on four SLO variants (wild-type (WT) enzyme, DM, and the two parental single mutants, L546A and L754A). DM is found to incorporate features of each parent, with the perturbation at position 546 predominantly influencing thermally activated motions that connect the active site to a protein-solvent interface, while mutation at position 754 disrupts the ligand field and solvation near the cofactor iron. However, the expanded active site in DM leads to more active site water molecules and their associated hydrogen bond network, and the individual features from L546A and L754A alone cannot explain the aggregate kinetic properties for DM. Using recently published QM/MM-derived ground-state SLO-substrate complexes for WT and DM, together with the thorough structural analyses presented herein, we propose that the impairment of DM is the combined result of a repositioning of the reactive carbon of linoleic acid substrate with regard to both the iron cofactor and a catalytically linked dynamic region of protein.


    Organizational Affiliation

    Department of Bioengineering and Therapeutic Science , University of California, San Francisco , San Francisco , California 94158 , United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seed linoleate 13S-lipoxygenase-1
A, B
839Glycine maxMutation(s): 2 
Gene Names: LOX1.1LOX1
EC: 1.13.11.12
Find proteins for P08170 (Glycine max)
Go to UniProtKB:  P08170
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.61α = 90
b = 92.809β = 94.11
c = 101.267γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM113432
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR022393-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM025765

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence