Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 84.39 kDa 
• Atom Count: 6338 
• Modelled Residue Count: 783 
• Deposited Residue Count: 786 
• Unique protein chains: 1

1AFW

THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE

• DOI: 10.2210/pdb1AFW/pdb

• Classification: THIOLASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1997-03-15 Released: 1997-06-16 
• Deposition Author(s): Mathieu, M., Wierenga, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.203 
• R-Value Observed: 0.187 

Literature

The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism.

Mathieu, M., Modis, Y., Zeelen, J.P., Engel, C.K., Abagyan, R.A., Ahlberg, A., Rasmussen, B., Lamzin, V.S., Kunau, W.H., Wierenga, R.K.

(1997) J Mol Biol 273: 714-728

• PubMed: 9402066 
• DOI: 10.1006/jmbi.1997.1331
• Primary Citation of Related Structures:  
  1AFW


• PubMed Abstract: 
  

The dimeric, peroxisomal 3-ketoacyl-CoA thiolase catalyses the conversion of 3-ketoacyl-CoA into acyl-CoA, which is shorter by two carbon atoms. This reaction is the last step of the beta-oxidation pathway. The crystal structure of unliganded peroxisomal thiolase of the yeast Saccharomyces cerevisiae has been refined at 1.8 A resolution. An unusual feature of this structure is the presence of two helices, completely buried in the dimer and sandwiched between two beta-sheets. The analysis of the structure shows that the sequences of these helices are not hydrophobic, but generate two amphipathic helices. The helix in the N-terminal domain exposes the polar side-chains to a cavity at the dimer interface, filled with structured water molecules. The central helix in the C-terminal domain exposes its polar residues to an interior polar pocket. The refined structure has also been used to predict the mode of binding of the substrate molecule acetoacetyl-CoA, as well as the reaction mechanism. From previous studies it is known that Cys125, His375 and Cys403 are important catalytic residues. In the proposed model the acetoacetyl group fits near the two catalytic cysteine residues, such that the oxygen atoms point towards the protein interior. The distance between SG(Cys125) and C3(acetoacetyl-CoA) is 3.7 A. The O2 atom of the docked acetoacetyl group makes a hydrogen bond to N(Gly405), which would favour the formation of the covalent bond between SG(Cys125) and C3(acetoacetyl-CoA) of the intermediate complex of the two-step reaction. The CoA moiety is proposed to bind in a groove on the surface of the protein molecule. Most of the interactions of the CoA molecule are with atoms of the loop domain. The three phosphate groups of the CoA moiety are predicted to interact with side-chains of lysine and arginine residues, which are conserved in the dimeric thiolases.

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Organizational Affiliation: 

EMBL, Meyerhofstrasse 1, Heidelberg, D69126, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-KETOACETYL-COA THIOLASE	A, B	393	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1.16
UniProt
Find proteins for P27796 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27796  Go to UniProtKB:  P27796

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A], D [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.203 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.17	α = 90
b = 92.65	β = 90
c = 116.72	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-03-15 
• Released Date: 1997-06-16 
Deposition Author(s): Mathieu, M., Wierenga, R.K.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance