4QWT | pdb_00004qwt

Anaerobic crystal structure of delta413-417:GS LOX in complex with arachidonate

• PDB DOI: https://doi.org/10.2210/pdb4QWT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plexaura homomalla
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-07-17 Released: 2014-09-24 
• Deposition Author(s): Neau, D.B., Newcomer, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Lipoxygenase in Complex with Substrate: THE ARACHIDONIC ACID-BINDING SITE OF 8R-LIPOXYGENASE.

Neau, D.B., Bender, G., Boeglin, W.E., Bartlett, S.G., Brash, A.R., Newcomer, M.E.

(2014) J Biological Chem 289: 31905-31913

• PubMed: 25231982 
• DOI: https://doi.org/10.1074/jbc.M114.599662
• Primary Citation Related Structures: 
  4QWT


• PubMed Abstract: 
  

  Lipoxygenases (LOX) play critical roles in mammalian biology in the generation of potent lipid mediators of the inflammatory response; consequently, they are targets for the development of isoform-specific inhibitors. The regio- and stereo-specificity of the oxygenation of polyunsaturated fatty acids by the enzymes is understood in terms of the chemistry, but structural observation of the enzyme-substrate interactions is lacking. Although several LOX crystal structures are available, heretofore the rapid oxygenation of bound substrate has precluded capture of the enzyme-substrate complex, leaving a gap between chemical and structural insights. In this report, we describe the 2.0 Å resolution structure of 8R-LOX in complex with arachidonic acid obtained under anaerobic conditions. Subtle rearrangements, primarily in the side chains of three amino acids, allow binding of arachidonic acid in a catalytically competent conformation. Accompanying experimental work supports a model in which both substrate tethering and cavity depth contribute to positioning the appropriate carbon at the catalytic machinery.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439, and.
Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803.
Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803,. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 321.74 kDa 
• Atom Count: 23,850 
• Modeled Residue Count: 2,725 
• Deposited Residue Count: 2,784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allene oxide synthase-lipoxygenase protein	A, B, C, D	696	Plexaura homomalla	Mutation(s): 2  EC: 1.13.11.40 (PDB Primary Data), 4.2.1 (UniProt)
UniProt
Find proteins for O16025 (Plexaura homomalla) Explore O16025  Go to UniProtKB:  O16025

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACD	YA [auth C]	ARACHIDONIC ACID C20 H32 O2 YZXBAPSDXZZRGB-DOFZRALJSA-N
GOL	AB [auth C], EA [auth B], FA [auth B], HA [auth B], HB [auth D], IA [auth B], JA [auth B], JB [auth D], M [auth A], N [auth A], O [auth A], P [auth A], SA [auth C], T [auth A], TA [auth C], UA [auth C], ZA [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	AA [auth B], BA [auth B], BB [auth C], CA [auth B], CB [auth D], DA [auth B], FB [auth D], GB [auth D], H [auth A], I [auth A], J [auth A], K [auth A], KB [auth D], L [auth A], LB [auth D], MB [auth D], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], U [auth A], V [auth A], W [auth A], X [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE2	DB [auth D], E [auth A], KA [auth C], Y [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	EB [auth D], F [auth A], G [auth A], LA [auth C], MA [auth C], S [auth A], XA [auth C], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	GA [auth B], IB [auth D], Q [auth A], R [auth A], VA [auth C], WA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.03	α = 90
b = 170.67	β = 95.36
c = 104.72	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
XSCALE	data scaling
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Neau, D.B., Newcomer, M.E.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2014-12-03
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description