4GAH

Human acyl-CoA thioesterases 4 in complex with undecan-2-one-CoA inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GAH/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-25 Released: 2012-08-29 
• Deposition Author(s): Lim, K., Pathak, M.C., Herzberg, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.190 

Starting Model: experimental

Literature

Correlation of structure and function in the human hotdog-fold enzyme hTHEM4.

Zhao, H., Lim, K., Choudry, A., Latham, J.A., Pathak, M.C., Dominguez, D., Luo, L., Herzberg, O., Dunaway-Mariano, D.

(2012) Biochemistry 51: 6490-6492

• PubMed: 22871024 
• DOI: https://doi.org/10.1021/bi300968n
• Primary Citation of Related Structures:  
  4GAH


• PubMed Abstract: 
  

  Human THEM4 (hTHEM4) is comprised of a catalytically active hotdog-fold acyl-CoA thioesterase domain and an N-terminal domain of unknown fold and function. hTHEM4 has been linked to Akt1 regulation and cell apoptosis. Herein, we report the X-ray structure of hHTEM4 bound with undecan-2-one-CoA. Structure guided mutagenesis was carried out to confirm the catalytic residues. The N-terminal domain is shown to be partially comprised of irregular and flexible secondary structure, reminiscent of a protein-binding domain. We demonstrate direct hTHEM4-Akt1 binding by immunoprecipitation and by inhibition of Akt1 kinase activity, thus providing independent evidence that hTHEM4 is an Akt1 negative regulator.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 50.74 kDa 
• Atom Count: 3,250 
• Modelled Residue Count: 367 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase superfamily member 4	A, B	209	Homo sapiens	Mutation(s): 0  Gene Names: CTMP, THEM4 EC: 3.1.2.20 (PDB Primary Data), 3.1.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T1C6 (Homo sapiens) Explore Q5T1C6  Go to UniProtKB:  Q5T1C6
PHAROS:  Q5T1C6 GTEx:  ENSG00000159445

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ET	C [auth A], D [auth B], E [auth B]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-[(2R)-2-oxidanylundecyl]sulfanylethylamino]propyl]amino]butyl] hydrogen phosphate C32 H58 N7 O17 P3 S LVZITIAGAKKXBV-XBRBJHMKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0ET	PDBBind:  4GAH	Kd: 800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.608	α = 90
b = 58.777	β = 90
c = 135.436	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Lim, K., Pathak, M.C., Herzberg, O.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description