PDBsum entry: 1wdk

Lyase,oxidoreductase/transferase

PDB id: 1wdk

Contents

Protein chains

708 a.a. *

390 a.a. *

Ligands

NAD ×2

N8E ×4

ACO ×2

Metals

_ZN

_HG ×2

Waters ×973

* Residue conservation analysis

PDB id:

1wdk

Name:

Lyase,oxidoreductase/transferase

Title:

Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form i (native2)

Structure:

Fatty oxidation complex alpha subunit. Chain: a, b. Synonym: fatty acid beta-oxidation multienzyme complex, alpha subunit. Ec: 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3. Engineered: yes. 3-ketoacyl-coa thiolase. Chain: c, d. Synonym: fatty acid beta-oxidation multienzyme complex,

Source:

Pseudomonas fragi. Organism_taxid: 296. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.203 R-free: 0.244

Authors:

M.Ishikawa,D.Tsuchiya,T.Oyama,Y.Tsunaka,K.Morikawa

Key ref:

M.Ishikawa et al. (2004). Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex. EMBO J, 23, 2745-2754. PubMed id: 15229654 DOI: 10.1038/sj.emboj.7600298

Date:

17-May-04 Release date: 27-Jul-04

Protein chains

P28793  (FADB_PSEFR) -  Fatty acid oxidation complex subunit alpha

Seq: 715 a.a.

Struc: 708 a.a.

Protein chains

P28790  (FADA_PSEFR) -  3-ketoacyl-CoA thiolase

Seq: 391 a.a.

Struc: 390 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.1.1.1.35 - 3-hydroxyacyl-CoA dehydrogenase.
• Reaction: (S)-3-hydroxyacyl-CoA + NAD⁺ = 3-oxoacyl-CoA + NADH

(S)-3-hydroxyacyl-CoA (Bound ligand (Het Group name = ACO) matches with 94.00% similarity) + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = 3-oxoacyl-CoA + NADH

• Enzyme class 2: Chains A, B: E.C.4.2.1.17 - Enoyl-CoA hydratase.
• Reaction: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H₂O

(3S)-3-hydroxyacyl-CoA (Bound ligand (Het Group name = ACO) matches with 94.00% similarity) = trans-2(or 3)-enoyl-CoA + H(2)O

• Enzyme class 3: Chains A, B: E.C.5.1.2.3 - 3-hydroxybutyryl-CoA epimerase.
• Reaction: (S)-3-hydroxybutanoyl-CoA = (R)-3-hydroxybutanoyl-CoA

(S)-3-hydroxybutanoyl-CoA (Bound ligand (Het Group name = ACO) matches with 94.00% similarity) = (R)-3-hydroxybutanoyl-CoA

• Enzyme class 4: Chains A, B: E.C.5.3.3.8 - Dodecenoyl-CoA isomerase.
• Reaction: (3Z)-dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA

(3Z)-dodec-3-enoyl-CoA (Bound ligand (Het Group name = ACO) matches with 83.00% similarity) = (2E)-dodec-2-enoyl-CoA

• Enzyme class 5: Chains C, D: E.C.2.3.1.16 - Acetyl-CoA C-acyltransferase.
• Reaction: Acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA

Acyl-CoA + acetyl-CoA (Bound ligand (Het Group name = ACO) corresponds exactly) = CoA + 3-oxoacyl-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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: metabolic process (6 terms)
• Biochemical function: catalytic activity (16 terms)

reference

DOI no: 10.1038/sj.emboj.7600298

EMBO J 23:2745-2754 (2004)

PubMed id: 15229654

Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex.

M.Ishikawa, D.Tsuchiya, T.Oyama, Y.Tsunaka, K.Morikawa.

ABSTRACT

The atomic view of the active site coupling termed channelling is a major subject in molecular biology. We have determined two distinct crystal structures of the bacterial multienzyme complex that catalyzes the last three sequential reactions in the fatty acid beta-oxidation cycle. The alpha2beta2 heterotetrameric structure shows the uneven ring architecture, where all the catalytic centers of 2-enoyl-CoA hydratase (ECH), L-3-hydroxyacyl-CoA dehydrogenase (HACD) and 3-ketoacyl-CoA thiolase (KACT) face a large inner solvent region. The substrate, anchored through the 3'-phosphate ADP moiety, allows the fatty acid tail to pivot from the ECH to HACD active sites, and finally to the KACT active site. Coupling with striking domain rearrangements, the incorporation of the tail into the KACT cavity and the relocation of 3'-phosphate ADP bring the reactive C2-C3 bond to the correct position for cleavage. The alpha-helical linker specific for the multienzyme contributes to the pivoting center formation and the substrate transfer through its deformation. This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex.

Selected figure(s)

Figure 2.
Figure 2 Active sites of three FOM components. Stereo diagrams show catalytic and hydrophobic residues around ligands in Form I. (A) Two C[8]E[5] molecules bound to each ECH of the dimer ( 1 and 2) in different modes, 'inside' (clear gray) and 'outside' (faint gray). The alkyl groups of two C[8]E[5] molecules are trapped with hydrophobic residues. Some parts of main chains (light brown) represent identical portions to rECH (Engel et al, 1996). (B) Ac-CoA and NAD^+ molecules bound to HACD in the Native3 crystal. The acetyl group of Ac-CoA points into the hydrophobic tunnel. (C) Ac-CoA molecules bound to the two KACT subunits. In Form II, the interaction of Arg369 with Val134 causes the 1 Å elevation (arrow) of the loop containing Val134 and Pro136 (cyan), and the subsequent rotation of the Trp70: 2 side chain (cyan).

Figure 5.
Figure 5 Homology model of the human TFE complex. (A) The symmetric TFE architecture, with the mutation sites (red spheres) relevant to various genetic diseases (Ibdah et al, 1998; Eaton et al, 2000). The arrowheads denote the HACD active sites. The inset indicates Val282, located in the interface between ECH in the -subunit and KACT in the -subunit. The insertion specific for TFE is depicted by dotted lines with asterisks. (B) Electrostatic surface representation showing the biased distribution of positive charges around the central solvent region.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2745-2754) copyright 2004.

Figures were selected by the author.