Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.50 kDa 
• Atom Count: 1260 
• Modelled Residue Count: 147 
• Deposited Residue Count: 156 
• Unique protein chains: 1

4JCZ

Human LTC4 synthase in complex with product analogs - implications for enzyme catalysis

• PDB DOI: 10.2210/pdb4JCZ/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2013-02-22 Released: 2014-01-01 
• Deposition Author(s): Niegowski, D., Rinaldo-Matthis, A., Haeggstrom, J.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.242 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs: IMPLICATIONS FOR THE ENZYME MECHANISM.

Niegowski, D., Kleinschmidt, T., Olsson, U., Ahmad, S., Rinaldo-Matthis, A., Haeggstrom, J.Z.

(2014) J Biol Chem 289: 5199-5207

• PubMed: 24366866 
• DOI: 10.1074/jbc.M113.534628
• Primary Citation of Related Structures:  
  4J7T, 4J7Y, 4JC7, 4JCZ, 4JRZ


• PubMed Abstract: 
  

Leukotriene (LT) C4 synthase (LTC4S) catalyzes the conjugation of the fatty acid LTA4 with the tripeptide GSH to produce LTC4, the parent compound of the cysteinyl leukotrienes, important mediators of asthma. Here we mutated Trp-116 in human LTC4S, a residue proposed to play a key role in substrate binding, into an Ala or Phe. Biochemical and structural characterization of these mutants along with crystal structures of the wild type and mutated enzymes in complex with three product analogs, viz. S-hexyl-, 4-phenyl-butyl-, and 2-hydroxy-4-phenyl-butyl-glutathione, provide new insights to binding of substrates and product, identify a new conformation of the GSH moiety at the active site, and suggest a route for product release, aided by Trp-116.

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Organizational Affiliation: 

From the Division of Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-107 77 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene C4 synthase	A	156	Homo sapiens	Mutation(s): 0  Gene Names: LTC4S EC: 4.4.1.20 (PDB Primary Data), 2.5.1 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens) Explore Q16873  Go to UniProtKB:  Q16873
PHAROS:  Q16873

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTX	J [auth A]	S-HEXYLGLUTATHIONE C16 H30 N3 O6 S HXJDWCWJDCOHDG-RYUDHWBXSA-O
PLM	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
PAM	D [auth A]	PALMITOLEIC ACID C16 H30 O2 SECPZKHBENQXJG-FPLPWBNLSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.242 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.281	α = 90
b = 170.281	β = 90
c = 170.281	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-22 
• Released Date: 2014-01-01 
Deposition Author(s): Niegowski, D., Rinaldo-Matthis, A., Haeggstrom, J.Z.

Revision History  

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Database references
• Version 1.2: 2014-03-12
  Changes: Database references