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: 23.78 kDa 
• Atom Count: 1436 
• Modelled Residue Count: 146 
• Deposited Residue Count: 156 
• Unique protein chains: 1

3PCV

Crystal structure analysis of human leukotriene C4 synthase at 1.9 angstrom resolution

• PDB DOI: 10.2210/pdb3PCV/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Schizosaccharomyces pombe
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2010-10-22 Released: 2011-03-16 
• Deposition Author(s): Saino, H., Ago, H., Miyano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

The catalytic architecture of leukotriene C4 synthase with two arginine residues

Saino, H., Ukita, Y., Ago, H., Irikura, D., Nisawa, A., Ueno, G., Yamamoto, M., Kanaoka, Y., Lam, B.K., Austen, K.F., Miyano, M.

(2011) J Biol Chem 286: 16392-16401

• PubMed: 21454538 
• DOI: 10.1074/jbc.M110.150177
• Primary Citation of Related Structures:  
  3PCV


• PubMed Abstract: 
  

Leukotriene (LT) C(4) and its metabolites, LTD(4) and LTE(4), are involved in the pathobiology of bronchial asthma. LTC(4) synthase is the nuclear membrane-embedded enzyme responsible for LTC(4) biosynthesis, catalyzing the conjugation of two substrates that have considerably different water solubility; that amphipathic LTA(4) as a derivative of arachidonic acid and a water-soluble glutathione (GSH). A previous crystal structure revealed important details of GSH binding and implied a GSH activating function for Arg-104. In addition, Arg-31 was also proposed to participate in the catalysis based on the putative LTA(4) binding model. In this study enzymatic assay with mutant enzymes demonstrates that Arg-104 is required for the binding and activation of GSH and that Arg-31 is needed for catalysis probably by activating the epoxide group of LTA(4).

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Related Citations: 

• Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis
  Ago, H., Kanaoka, Y., Irikura, D., Lam, B.K., Shimamura, T., Austen, K.F., Miyano, M.
  (2007) Nature 448: 609

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Organizational Affiliation: 

Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan.

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
LMT	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
GSH	B [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
SO4	V [auth A], W [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	N [auth A], O [auth A], P [auth A], Q [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	R [auth A], S [auth A], T [auth A], U [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.0295	α = 90
b = 168.0295	β = 90
c = 168.0295	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-22 
• Released Date: 2011-03-16 
Deposition Author(s): Saino, H., Ago, H., Miyano, M.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-14
  Changes: Database references, Non-polymer description