PDBsum entry: 1qfl

Transferase

PDB id: 1qfl

Contents

Protein chains

389 a.a. *

Ligands

SO4 ×6

COA ×4

Waters ×718

* Residue conservation analysis

PDB id:

1qfl

Name:

Transferase

Title:

Biosynthetic thiolase from zoogloea ramigera in complex with a reaction intermediate.

Structure:

Protein (acetoacetyl-coa thiolase). Chain: a, b, c, d. Fragment: residues 4-392. Synonym: biosynthetic thiolase. Engineered: yes. Other_details: cys89 is acetylated

Source:

Zoogloea ramigera. Organism_taxid: 350. Expressed in: escherichia coli. Expression_system_taxid: 562. (Pharmacia)

Biol. unit:

Tetramer (from PQS)

Resolution:

1.92Å R-factor: 0.209 R-free: 0.256

Authors:

Y.Modis,R.K.Wierenga

Key ref:

Y.Modis and R.K.Wierenga (1999). A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism. Structure, 7, 1279-1290. PubMed id: 10545327 DOI: 10.1016/S0969-2126(00)80061-1

Date:

12-Apr-99 Release date: 19-Apr-00

Protein chains

P07097  (THIL_ZOORA) -  Acetyl-CoA acetyltransferase

Seq: 392 a.a.

Struc: 389 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.1.9 - Acetyl-CoA C-acetyltransferase.
• Pathway: Mevalonate Biosynthesis
• Reaction: 2 acetyl-CoA = CoA + acetoacetyl-CoA

2 × acetyl-CoA (Bound ligand (Het Group name = COA) matches with 94.00% similarity) = CoA + acetoacetyl-CoA

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (5 terms)

reference

DOI no: 10.1016/S0969-2126(00)80061-1

Structure 7:1279-1290 (1999)

PubMed id: 10545327

A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism.

Y.Modis, R.K.Wierenga.

ABSTRACT

BACKGROUND: Thiolases are ubiquitous and form a large family of dimeric or tetrameric enzymes with a conserved, five-layered alphabetaalphabetaalpha catalytic domain. Thiolases can function either degradatively, in the beta-oxidation pathway of fatty acids, or biosynthetically. Biosynthetic thiolases catalyze the biological Claisen condensation of two molecules of acetyl-CoA to form acetoacetyl-CoA. This is one of the fundamental categories of carbon skeletal assembly patterns in biological systems and is the first step in a wide range of biosynthetic pathways, including those that generate cholesterol, steroid hormones, and various energy-storage molecules. RESULTS: The crystal structure of the tetrameric biosynthetic thiolase from Zoogloea ramigera has been determined at 2.0 A resolution. The structure contains a striking and novel 'cage-like' tetramerization motif, which allows for some hinge motion of the two tight dimers with respect to each other. The protein crystals were flash-frozen after a short soak with the enzyme's substrate, acetoacetyl-CoA. A reaction intermediate was thus trapped: the enzyme tetramer is acetylated at Cys89 and has a CoA molecule bound in each of its active-site pockets. CONCLUSIONS: The shape of the substrate-binding pocket reveals the basis for the short-chain substrate specificity of the enzyme. The active-site architecture, and in particular the position of the covalently attached acetyl group, allow a more detailed reaction mechanism to be proposed in which Cys378 is involved in both steps of the reaction. The structure also suggests an important role for the thioester oxygen atom of the acetylated enzyme in catalysis.

Selected figure(s)

Figure 4.
Figure 4. Contact distances between the CoA molecule and subunit B of biosynthetic thiolase. The catalytic residues Cys89, His348 and Cys378 are also shown. Water molecules are represented as gray circles. There is only one direct hydrogen bond between the protein and the CoA molecule, between Ser247 and the NP2 atom of CoA. Most other contacts are mediated by one or more water molecules. Distances are given in Ångstroms.

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1279-1290) copyright 1999.

Figure was selected by an automated process.