Crystal structure of tt0168 from Thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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Structural basis of the substrate specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer

Hisanaga, Y.Ago, H.Nakagawa, N.Hamada, K.Ida, K.Yamamoto, M.Hori, T.Arii, Y.Sugahara, M.Kuramitsu, S.Yokoyama, S.Miyano, M.

(2004) J Biol Chem 279: 31717-31726

  • DOI: https://doi.org/10.1074/jbc.M400100200
  • Primary Citation of Related Structures:  
    1ULT, 1V25, 1V26

  • PubMed Abstract: 

    Long chain fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of long chain fatty acyl-CoA esters. We report the first crystal structures of long chain fatty acyl-CoA synthetase homodimer (LC-FACS) from Thermus thermophilus HB8 (ttLC-FACS), including complexes with the ATP analogue adenosine 5'-(beta,gamma-imido) triphosphate (AMP-PNP) and myristoyl-AMP. ttLC-FACS is a member of the adenylate forming enzyme superfamily that catalyzes the ATP-dependent acylation of fatty acid in a two-step reaction. The first reaction step was shown to propagate in AMP-PNP complex crystals soaked with myristate solution. Myristoyl-AMP was identified as the intermediate. The AMP-PNP and the myristoyl-AMP complex structures show an identical closed conformation of the small C-terminal domains, whereas the uncomplexed form shows a variety of open conformations. Upon ATP binding, the fatty acid-binding tunnel gated by an aromatic residue opens to the ATP-binding site. The gated fatty acid-binding tunnel appears only to allow one-way movement of the fatty acid during overall catalysis. The protein incorporates a hydrophobic branch from the fatty acid-binding tunnel that is responsible for substrate specificity. Based on these high resolution crystal structures, we propose a unidirectional Bi Uni Uni Bi Ping-Pong mechanism for the two-step acylation by ttLC-FACS.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
long chain fatty acid-CoA ligase
A, B
541Thermus thermophilusMutation(s): 0 
Find proteins for Q5SKN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKN9 
Go to UniProtKB:  Q5SKN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKN9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CIT

Download Ideal Coordinates CCD File 
C6 H8 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.952α = 90
b = 124.687β = 90
c = 212.471γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations