3LEO

Structure of human Leukotriene C4 synthase mutant R31Q in complex with glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMTClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view detailsBest fitted PLMClick on this verticalbar to view detailsBest fitted PAMClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Arginine 104 is a key catalytic residue in leukotriene C4 synthase.

Rinaldo-Matthis, A.Wetterholm, A.Martinez Molina, D.Holm, J.Niegowski, D.Ohlson, E.Nordlund, P.Morgenstern, R.Haeggstrom, J.Z.

(2010) J Biol Chem 285: 40771-40776

  • DOI: https://doi.org/10.1074/jbc.M110.105940
  • Primary Citation of Related Structures:  
    3LEO

  • PubMed Abstract: 

    Human leukotriene C(4) synthase (hLTC(4)S) is an integral membrane enzyme that conjugates leukotriene (LT) A(4) with glutathione to form LTC(4), a precursor to the cysteinyl leukotrienes (LTC(4), LTD(4), and LTE(4)) that are involved in the pathogenesis of human bronchial asthma. From the crystal structure of hLTC(4)S, Arg-104 and Arg-31 have been implicated in the conjugation reaction. Here, we used site-directed mutagenesis, UV spectroscopy, and x-ray crystallography to examine the catalytic role of Arg-104 and Arg-31. Exchange of Arg-104 with Ala, Ser, Thr, or Lys abolished 94.3-99.9% of the specific activity against LTA(4). Steady-state kinetics of R104A and R104S revealed that the K(m) for GSH was not significantly affected. UV difference spectra of the binary enzyme-GSH complex indicated that GSH ionization depends on the presence of Arg-104 because no thiolate signal, with λ(max) at 239 nm, could be detected using R104A or R104S hLTC(4)S. Apparently, the interaction of Arg-104 with the thiol group of GSH reduces its pK(a) to allow formation of a thiolate anion and subsequent nucleophilic attack at C6 of LTA(4). On the other hand, exchange of Arg-31 with Ala or Glu reduced the catalytic activity of hLTC(4)S by 88 and 70%, respectively, without significantly affecting the k(cat)/K(m) values for GSH, and a crystal structure of R31Q hLTC(4)S (2.1 Å) revealed a Gln-31 side chain pointing away from the active site. We conclude that Arg-104 plays a critical role in the catalytic mechanism of hLTC(4)S, whereas a functional role of Arg-31 seems more elusive. Because Arg-104 is a conserved residue, our results pertain to other homologous membrane proteins and represent a structure-function paradigm probably common to all microsomal GSH transferases.


  • Organizational Affiliation

    Division of Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene C4 synthase155Homo sapiensMutation(s): 1 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16873
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
N [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
GSH
Query on GSH

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M [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
PLM
Query on PLM

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C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
PAM
Query on PAM

Download Ideal Coordinates CCD File 
B [auth A],
P [auth A]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
SO4
Query on SO4

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F [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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O [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI
Query on NI

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K [auth A],
L [auth A]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.54α = 90
b = 169.54β = 90
c = 169.54γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMTClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view detailsBest fitted PLMClick on this verticalbar to view detailsBest fitted PAMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Non-polymer description
  • Version 1.3: 2012-12-26
    Changes: Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description