2PNO

Crystal structure of human leukotriene C4 synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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: 609-612

  • DOI: https://doi.org/10.1038/nature05936
  • Primary Citation of Related Structures:  
    2PNO

  • PubMed Abstract: 

    The cysteinyl leukotrienes, namely leukotriene (LT)C4 and its metabolites LTD4 and LTE4, the components of slow-reacting substance of anaphylaxis, are lipid mediators of smooth muscle constriction and inflammation, particularly implicated in bronchial asthma. LTC4 synthase (LTC4S), the pivotal enzyme for the biosynthesis of LTC4 (ref. 10), is an 18-kDa integral nuclear membrane protein that belongs to a superfamily of membrane-associated proteins in eicosanoid and glutathione metabolism that includes 5-lipoxygenase-activating protein, microsomal glutathione S-transferases (MGSTs), and microsomal prostaglandin E synthase 1 (ref. 13). LTC4S conjugates glutathione to LTA4, the endogenous substrate derived from arachidonic acid through the 5-lipoxygenase pathway. In contrast with MGST2 and MGST3 (refs 15, 16), LTC4S does not conjugate glutathione to xenobiotics. Here we show the atomic structure of human LTC4S in a complex with glutathione at 3.3 A resolution by X-ray crystallography and provide insights into the high substrate specificity for glutathione and LTA4 that distinguishes LTC4S from other MGSTs. The LTC4S monomer has four transmembrane alpha-helices and forms a threefold symmetric trimer as a unit with functional domains across each interface. Glutathione resides in a U-shaped conformation within an interface between adjacent monomers, and this binding is stabilized by a loop structure at the top of the interface. LTA4 would fit into the interface so that Arg 104 of one monomer activates glutathione to provide the thiolate anion that attacks C6 of LTA4 to form a thioether bond, and Arg 31 in the neighbouring monomer donates a proton to form a hydroxyl group at C5, resulting in 5(S)-hydroxy-6(R)-S-glutathionyl-7,9-trans-11,14-cis-eicosatetraenoic acid (LTC4). These findings provide a structural basis for the development of LTC4S inhibitors for a proinflammatory pathway mediated by three cysteinyl leukotriene ligands whose stability and potency are different and by multiple cysteinyl leukotriene receptors whose functions may be non-redundant.


  • Organizational Affiliation

    Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene C4 synthase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
156Homo sapiensMutation(s): 0 
EC: 4.4.1.20
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens)
Explore Q16873 
Go to UniProtKB:  Q16873
PHAROS:  Q16873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16873
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth F]
AC [auth L]
BA [auth B]
BB [auth F]
AA [auth B],
AB [auth F],
AC [auth L],
BA [auth B],
BB [auth F],
BC [auth L],
CA [auth B],
CB [auth F],
CC [auth L],
EA [auth C],
EB [auth G],
FA [auth C],
FB [auth G],
GA [auth C],
GB [auth G],
HA [auth C],
HB [auth G],
IA [auth C],
IB [auth G],
KA [auth D],
KB [auth H],
LA [auth D],
LB [auth H],
MA [auth D],
N [auth A],
NB [auth I],
O [auth A],
OA [auth E],
OB [auth I],
P [auth A],
PA [auth E],
PB [auth I],
Q [auth A],
QA [auth E],
QB [auth I],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
SB [auth J],
T [auth A],
TA [auth E],
TB [auth J],
U [auth A],
UA [auth E],
VA [auth E],
VB [auth K],
W [auth B],
WA [auth E],
WB [auth K],
X [auth B],
XA [auth E],
Y [auth B],
YB [auth L],
Z [auth B],
ZA [auth F],
ZB [auth L]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
DA [auth C]
DB [auth G]
JA [auth D]
JB [auth H]
M [auth A]
DA [auth C],
DB [auth G],
JA [auth D],
JB [auth H],
M [auth A],
MB [auth I],
NA [auth E],
RB [auth J],
UB [auth K],
V [auth B],
XB [auth L],
YA [auth F]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.5α = 90
b = 293.9β = 90
c = 206.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2011-12-07
    Changes: Non-polymer description
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description