Crystal structure of the human squalene synthase F288L mutant in complex with presqualene pyrophosphate

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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This is version 1.2 of the entry. See complete history


Structural insights into the catalytic mechanism of human squalene synthase.

Liu, C.I.Jeng, W.Y.Chang, W.J.Shih, M.F.Ko, T.P.Wang, A.H.J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 231-241

  • DOI: https://doi.org/10.1107/S1399004713026230
  • Primary Citation of Related Structures:  
    3WEF, 3WEG, 3WEH, 3WEI, 3WEJ, 3WEK

  • PubMed Abstract: 

    Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step reductive `head-to-head' condensation of two molecules of farnesyl pyrophosphate to form squalene using presqualene diphosphate (PSPP) as an intermediate. In this paper, the structures of human SQS and its mutants in complex with several substrate analogues and intermediates coordinated with Mg2+ or Mn2+ are presented, which stepwise delineate the biosynthetic pathway. Extensive study of the SQS active site has identified several critical residues that are involved in binding reduced nicotinamide dinucleotide phosphate (NADPH). Based on mutagenesis data and a locally closed (JK loop-in) structure observed in the hSQS-(F288L)-PSPP complex, an NADPH-binding model is proposed for SQS. The results identified four major steps (substrate binding, condensation, intermediate formation and translocation) of the ordered sequential mechanisms involved in the `1'-1' isoprenoid biosynthetic pathway. These new findings clarify previous hypotheses based on site-directed mutagenesis and biochemical analysis.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Squalene synthase343Homo sapiensMutation(s): 1 
Gene Names: FDFT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P37268 (Homo sapiens)
Explore P37268 
Go to UniProtKB:  P37268
PHAROS:  P37268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37268
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PS7

Download Ideal Coordinates CCD File 
C [auth A]{(1R,2R,3R)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-2-methyl-3-[(1E,5E)-2,6,10-trimethylundeca-1,5,9-trien-1-yl]cyclopropyl}methyl trihydrogen diphosphate
C30 H52 O7 P2
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.192α = 90
b = 106.502β = 90
c = 32.988γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description