1V25

Crystal structure of tt0168 from Thermus thermophilus HB8

• PDB DOI:  https://doi.org/10.2210/pdb1V25/pdb

• Classification: LIGASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-07 Released: 2004-07-27 
• Deposition Author(s): Hisanaga, Y., Ago, H., Nakatsu, T., Hamada, K., Ida, K., Kanda, H., Yamamoto, M., Hori, T., Arii, Y., Sugahara, M., Kuramitsu, S., Yokoyama, S., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.240 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 

Literature

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

• PubMed: 15145952 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 120.36 kDa 
• Atom Count: 8,236 
• Modelled Residue Count: 998 
• Deposited Residue Count: 1,082 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
long-chain-fatty-acid-CoA synthetase	A, B	541	Thermus thermophilus	Mutation(s): 0  EC: 6.2.1.3
UniProt
Find proteins for Q5SKN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKN9  Go to UniProtKB:  Q5SKN9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.240 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.52	α = 90
b = 101.151	β = 90
c = 176.487	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Hisanaga, Y., Ago, H., Nakatsu, T., Hamada, K., Ida, K., Kanda, H., Yamamoto, M., Hori, T., Arii, Y., Sugahara, M., Kuramitsu, S., Yokoyama, S., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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