3FG4 | pdb_00003fg4

Crystal structure of Delta413-417:GS I805A LOX

PDB DOI: https://doi.org/10.2210/pdb3FG4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Plexaura homomalla
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes mpstruc

Deposited: 2008-12-04 Released: 2009-08-18
Deposition Author(s): Neau, D.B., Newcomer, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.239 (Depositor), 0.236 (DCC)
R-Value Work:
0.168 (Depositor), 0.167 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.

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

(2009) Biochemistry 48: 7906-7915

PubMed: 19594169 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi900084m
Primary Citation Related Structures:
3FG1, 3FG3, 3FG4

PubMed Abstract:
Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors. We report here the 1.85 A resolution structure of an 8R-lipoxygenase from Plexaura homomalla, an enzyme with a sequence approximately 40% identical to that of human 5-LOX. The structure reveals a U-shaped channel, defined by invariant amino acids, that would allow substrate access to the catalytic iron. We demonstrate that mutations within the channel significantly impact enzyme activity and propose a novel model for substrate binding potentially applicable to other members of this enzyme family.

Organizational Affiliation

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

Macromolecule Content

Total Structure Weight: 322.38 kDa
Atom Count: 23,613
Modeled Residue Count: 2,717
Deposited Residue Count: 2,784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allene oxide synthase-lipoxygenase protein	A, B, C, D	696	Plexaura homomalla	Mutation(s): 3 EC: 1.13.11.40 (PDB Primary Data), 4.2.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for O16025 (Plexaura homomalla) Explore O16025 Go to UniProtKB: O16025
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O16025
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACD Query on ACD Download:Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain NA [auth C] SDF format, chain H [auth A] SDF format, chain BA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain NA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth B]	BA [auth B], DB [auth D], H [auth A], NA [auth C]	ARACHIDONIC ACID C₂₀ H₃₂ O₂ YZXBAPSDXZZRGB-DOFZRALJSA-N		Interactions Focus chain BA [auth B] Focus chain DB [auth D] Focus chain H [auth A] Focus chain NA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain DB [auth D] Focus chain H [auth A] Focus chain NA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain JB [auth D] SDF format, chain WA [auth C] SDF format, chain YA [auth C] SDF format, chain Y [auth A] SDF format, chain XA [auth C] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain KB [auth D] SDF format, chain IB [auth D] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain WA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain WA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	GA [auth B] HA [auth B] IA [auth B] IB [auth D] JB [auth D] GA [auth B], HA [auth B], IA [auth B], IB [auth D], JB [auth D], KB [auth D], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], UA [auth C], V [auth A], VA [auth C], WA [auth C], XA [auth C], Y [auth A], YA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain QA [auth C] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HB [auth D] SDF format, chain GB [auth D] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B] DA [auth B] EA [auth B] EB [auth D] FA [auth B] CA [auth B], DA [auth B], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GB [auth D], HB [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain KA [auth C] SDF format, chain E [auth A] SDF format, chain BB [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain BB [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain BB [auth D]	BB [auth D], E [auth A], KA [auth C], Z [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain E [auth A] Focus chain KA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain BB [auth D] Focus chain E [auth A] Focus chain KA [auth C] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain X [auth A] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain CB [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain CB [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain X [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain CB [auth D]	AA [auth B] AB [auth C] CB [auth D] F [auth A] G [auth A] AA [auth B], AB [auth C], CB [auth D], F [auth A], G [auth A], LA [auth C], MA [auth C], X [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain CB [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain X [auth A] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain CB [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain X [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain LB [auth D] SDF format, chain ZA [auth C] SDF format, chain W [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain ZA [auth C] MOL2 format, chain W [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain LB [auth D] mmCIF format, chain ZA [auth C] mmCIF format, chain W [auth A]	JA [auth B], LB [auth D], W [auth A], ZA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth B] Focus chain LB [auth D] Focus chain W [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain JA [auth B] Focus chain LB [auth D] Focus chain W [auth A] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.239 (Depositor), 0.236 (DCC)
R-Value Work: 0.168 (Depositor), 0.167 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.361	α = 90
b = 170.382	β = 95.51
c = 104.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Neau, D.B.

Newcomer, M.E.

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description