PDBsum entry 2d3t

Lyase, oxidoreductase/transferase

PDB id: 2d3t

Contents

Protein chains

708 a.a. *

390 a.a. *

Ligands

NAD ×2

ACO ×2

* Residue conservation analysis

PDB id:

2d3t

Name:

Lyase, oxidoreductase/transferase

Title:

Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form v

Structure:

Fatty oxidation complex alpha subunit. Chain: a, b. 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 oxidation complex beta subunit, beta-ketothiolase, acetyl-coa acyltransferase. Engineered: yes

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

3.40Å R-factor: 0.242 R-free: 0.295

Authors:

D.Tsuchiya,N.Shimizu,M.Ishikawa,Y.Suzuki,K.Morikawa

Key ref:

D.Tsuchiya et al. (2006). Ligand-Induced Domain Rearrangement of Fatty Acid beta-Oxidation Multienzyme Complex. Structure, 14, 237-246. PubMed id: 16472743 DOI: 10.1016/j.str.2005.10.011

Date:

01-Oct-05 Release date: 21-Feb-06

Protein chains

P28793  (FADB_PSEFR) -  Fatty acid oxidation complex subunit alpha from Pseudomonas fragi

Seq: 715 a.a.

Struc: 708 a.a.

Protein chains

P28790  (FADA_PSEFR) -  3-ketoacyl-CoA thiolase from Pseudomonas fragi

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: a (3S)-3-hydroxyacyl-CoA + NAD⁺ = a 3-oxoacyl-CoA + NADH + H⁺

(3S)-3-hydroxyacyl-CoA (Bound ligand (Het Group name = ACO) matches with 94.44% similarity) + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = 3-oxoacyl-CoA + NADH + H(+)

• Enzyme class 2: Chains A, B: 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 = ACO) matches with 94.44% similarity) = (2E)-enoyl-CoA + H2O

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

(3S)-3-hydroxybutanoyl-CoA = (3R)-3-hydroxybutanoyl-CoA (Bound ligand (Het Group name = ACO) matches with 94.44% similarity)

• Enzyme class 4: Chains A, B: 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
• Enzyme class 5: Chains C, D: E.C.2.3.1.16 - acetyl-CoA C-acyltransferase.
• Reaction: an acyl-CoA + acetyl-CoA = a 3-oxoacyl-CoA + CoA

acyl-CoA (Bound ligand (Het Group name = ACO) corresponds exactly) + acetyl-CoA = 3-oxoacyl-CoA + 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: 10.1016/j.str.2005.10.011

Structure 14:237-246 (2006)

PubMed id: 16472743

Ligand-Induced Domain Rearrangement of Fatty Acid beta-Oxidation Multienzyme Complex.

D.Tsuchiya, N.Shimizu, M.Ishikawa, Y.Suzuki, K.Morikawa.

ABSTRACT

The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.

Selected figure(s)

Figure 2.
Figure 2. Substrate Recognition in the a Subunit
(A) Local structures around the adenine base binding site in the a subunit, observed in forms I (red) and V (orange, green). The bound ligand is acetyl-CoA, which is an analog of 3-hydroxyacyl-CoA.
(B and C) The corresponding structures of the (B) proximal and (C) distal subunits in form II.
(D) Superimposition of the two a subunits in the apparently symmetric form I, in which the acetyl-CoA (the red space-filling model) was observed. The ligand bound subunit (red) is more open than the unliganded one (blue). As a consequence, only the aC domain exhibits a significant difference. The circle with the broken line indicates the adenine base moiety in (A).

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 237-246) copyright 2006.

Figure was selected by an automated process.