1AFW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1006/jmbi.1997.1331

  • 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 peroxis ...

    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.


    Organizational Affiliation

    EMBL, Meyerhofstrasse 1, Heidelberg, D69126, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-KETOACETYL-COA THIOLASE
A, B
393Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: POT1 (FOX3, POX3)
EC: 2.3.1.16
Find proteins for P27796 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: POT1
Go to UniProtKB:  P27796
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.170α = 90.00
b = 92.650β = 90.00
c = 116.720γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
SCALEPACKdata scaling
TNTphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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