PDBsum entry 2dub

Lyase

PDB id: 2dub

Contents

Protein chains

(+ 0 more) 254 a.a. *

Ligands

CO8 ×4

Waters ×436

* Residue conservation analysis

PDB id:

2dub

Name:

Lyase

Title:

Enoyl-coa hydratase complexed with octanoyl-coa

Structure:

2-enoyl-coa hydratase. Chain: a, b, c, d, e, f. Synonym: crotonase, enoyl-coa hydratase 1. Other_details: cocrystallized with octanoyl-coa

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: liver. Cellular_location: mitochondria

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.40Å R-factor: 0.204 R-free: 0.260

Authors:

C.K.Engel,R.K.Wierenga

Key ref:

C.K.Engel et al. (1998). The crystal structure of enoyl-CoA hydratase complexed with octanoyl-CoA reveals the structural adaptations required for binding of a long chain fatty acid-CoA molecule. J Mol Biol, 275, 847-859. PubMed id: 9480773 DOI: 10.1006/jmbi.1997.1491

Date:

28-Apr-97 Release date: 29-Apr-98

Protein chains

P14604  (ECHM_RAT) -  Enoyl-CoA hydratase, mitochondrial from Rattus norvegicus

Seq: 290 a.a.

Struc: 254 a.a.

Enzyme reactions

• Enzyme class 1: E.C.4.2.1.17 - enoyl-CoA hydratase.
• Reaction:
  1. a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O
  2. a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O

(3S)-3-hydroxyacyl-CoA (Bound ligand (Het Group name = CO8) matches with 88.14% similarity) = (2E)-enoyl-CoA + H2O

• Enzyme class 2: E.C.5.3.3.8 - Delta(3)-Delta(2)-enoyl-CoA isomerase.
• Reaction:
  1. a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA
  2. a (3E)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1006/jmbi.1997.1491

J Mol Biol 275:847-859 (1998)

PubMed id: 9480773

The crystal structure of enoyl-CoA hydratase complexed with octanoyl-CoA reveals the structural adaptations required for binding of a long chain fatty acid-CoA molecule.

C.K.Engel, T.R.Kiema, J.K.Hiltunen, R.K.Wierenga.

ABSTRACT

The structure of the hexameric rat mitochondrial enoyl-Coenzyme A (CoA) hydratase, co-crystallised with the inhibitor octanoyl-CoA, has been refined at a resolution of 2.4 A. Enoyl-CoA hydratase catalyses the hydration of 2,3-unsaturated enoyl-CoA thioesters. In the crystal structure only four of the six active sites of the hexamer in the asymmetric unit are occupied with a ligand molecule, showing an unliganded and a liganded active site within the same crystal form. While the protein assembly and fold is identical to the previously solved acetoacetyl-CoA complex, differences are observed close to the fatty acid binding pocket due to the different nature of the ligands. The fatty acid tail of octanoyl-CoA is bound in an extended conformation. This is possible because a high B-factor loop, which separates in the acetoacetyl-CoA complex the binding pocket of the acetoacetyl-CoA fatty acid tail from the intertrimer space, has moved aside to allow binding of the longer octanoyl-CoA moiety. The movement of this loop opens a tunnel which traverses the complete subunit from the solvent space to the intertrimer space. The conformation of the catalytic residues is identical, in both structures as well as in the liganded and the unliganded active sites. In the unliganded active sites a water molecules is bound between the two catalytic glutamate, residues Glu144 and Glu164. After superposition of a liganded active site on an unliganded active site this water molecule is close to the carbon centre that becomes hydroxylated in the hydratase reaction. These findings support the idea that the active site is rigid and that the catalytic residues and the water molecule, as seen in the unliganded active site, are pre-positioned for very efficient catalysis.

Selected figure(s)

Figure 1.
Figure 1. A, The reaction catalysed by enoyl-CoA hydratase. B, Covalent structure of the acetoacetyl moiety of the inhibitor acetoacetyl-CoA. On the basis of spectroscopic measurements of acetoacetyl-CoA bound to hydratase it was concluded that the 2,3-enolate form is the inhibitory species of the hydratase reaction (Waterson & Hill, 1972). C, Covalent structure of the octanoyl moiety of the inhibitor octanoyl-CoA. D, Schematic drawing of Coenzyme A.

Figure 5.
Figure 5. Stereo picture of the active site of the unliganded subunit D. Superimposed is the omit (Fo - Fc, aC density from a model where the active site residues and the water molecule between them were removed. The distances between this water molecule (X39) and the catalytic residues are indicated. The map is contoured at 3s.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 275, 847-859) copyright 1998.

Figures were selected by an automated process.