PDBsum entry: 1afw

Thiolase

PDB id: 1afw

Contents

Protein chains

390 a.a. *

Ligands

MRD ×2

Waters ×448

* Residue conservation analysis

PDB id:

1afw

Name:

Thiolase

Title:

The 1.8 angstrom crystal structure of the dimeric peroxisomal thiolase of saccharomyces cerevisiae

Structure:

3-ketoacetyl-coa thiolase. Chain: a, b. Ec: 2.3.1.16

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organelle: peroxisome. Cellular_location: peroxisome

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.187 R-free: 0.240

Authors:

M.Mathieu,R.K.Wierenga

Key ref:

M.Mathieu et al. (1997). The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. J Mol Biol, 273, 714-728. PubMed id: 9402066 DOI: 10.1006/jmbi.1997.1331

Date:

15-Mar-97 Release date: 16-Jun-97

Protein chains

P27796  (THIK_YEAST) -  3-ketoacyl-CoA thiolase, peroxisomal

Seq: 417 a.a.

Struc: 390 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.1.16 - Acetyl-CoA C-acyltransferase.
• Reaction: Acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: peroxisome (2 terms)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1006/jmbi.1997.1331

J Mol Biol 273:714-728 (1997)

PubMed id: 9402066

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

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

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.

Selected figure(s)

Figure 7.
Figure 7. Schematic picture indicating the relative position of the modelled acetoacetyl group and the catalytic residues. Important hydrogen bonds are highlighted. The (SG(Cys125)-C1) and the (SG(Cys125)-C3) distances are 3.7 Å and 3.7 Å, respectively. The (SG(Cys403)-C2) distance is 4.5 Å.

Figure 9.
Figure 9. The proposed reaction mechanism for the degradative reaction of thiolase. Four steps are emphasised: 1, the formation of the covalent intermediate; 2, the replacement of acetyl-CoA by CoA; 3, the activation of CoA; and 4, the formation of the product.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 273, 714-728) copyright 1997.

Figures were selected by an automated process.