PDBsum entry 2bac

Isomerase

PDB id: 2bac

Contents

Protein chain

423 a.a. *

Ligands

SO4 ×2

FAD

ODT

Waters ×467

* Residue conservation analysis

PDB id:

2bac

Name:

Isomerase

Title:

Crystal structure of cla-producing fatty acid isomerase from p. Acnes

Structure:

Putative aminooxidase. Chain: a. Synonym: fatty acid isomerase. Engineered: yes

Source:

Propionibacterium acnes. Organism_taxid: 1747. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.161 R-free: 0.228

Authors:

M.G.Rudolph,A.Liavonchanka

Key ref:

A.Liavonchanka et al. (2006). Structure and mechanism of the Propionibacterium acnes polyunsaturated fatty acid isomerase. Proc Natl Acad Sci U S A, 103, 2576-2581. PubMed id: 16477020 DOI: 10.1073/pnas.0510144103

Date:

14-Oct-05 Release date: 31-Jan-06

Protein chain

Q6A8X5  (Q6A8X5_CUTAK) -  Aminooxidase from Cutibacterium acnes (strain DSM 16379 / KPA171202)

Seq: 424 a.a.

Struc: 423 a.a.

DOI no: 10.1073/pnas.0510144103

Proc Natl Acad Sci U S A 103:2576-2581 (2006)

PubMed id: 16477020

Structure and mechanism of the Propionibacterium acnes polyunsaturated fatty acid isomerase.

A.Liavonchanka, E.Hornung, I.Feussner, M.G.Rudolph.

ABSTRACT

Conjugated linoleic acids (CLAs) affect body fat gain, carcinogenesis, insulin resistance, and lipid peroxidation in mammals. Several isomers of CLA exist, of which the (9Z, 11E) and (10E, 12Z) isomers have beneficial effects on human metabolism but are scarce in foods. Bacterial polyunsaturated fatty acid isomerases are promising biotechnological catalysts for CLA production. We describe six crystal structures of the Propionibacterium acnes polyunsaturated fatty acid isomerase PAI in apo- and product-bound forms. The three-domain flavoprotein has previously undescribed folds outside the FAD-binding site. Conformational changes in a hydrophobic channel toward the active site reveal a unique gating mechanism for substrate specificity. The geometry of the substrate-binding site explains the length preferences for C18 fatty acids. A catalytic mechanism for double-bond isomerization is formulated that may be altered to change substrate specificity for syntheses of rare CLAs from easily accessible precursors.

Selected figure(s)

Figure 1.
Fig. 1. The PAI reaction and structure. (a) Reaction catalyzed by PAI. (b) [A]-weighted mF[o] – DF[c] omit electron density maps contoured at 2 of FAD and a side-on view of the isoalloxazine ring (Inset). (c) Architecture of PAI with the FAD-binding domain colored in magenta, domain 2 in red, and domain 3 in blue. FAD and PEG 400 are shown as stick models in this stereo figure. (d) PAI structural analogs: polyaminooxidase (PDB ID code 1RSG) (Left), UDP-galactopyranose mutase (1I8T) (Center), and guanine nucleotide dissociation inhibitor (1GND) (Right). The domains are colored as for PAI but in lighter hue.

Figure 3.
Fig. 3. Substrate entry channel and gating mechanism in PAI. (a) The surface potential of PAI shows an electropositive area localized at the entrance of the channel that is created by Lys-85, Arg-87, Lys-102, and Lys-195. The PEG 400 molecule marks the entry of the channel. (b) The molecular surface (blue) of part of the PEG 400 molecule bound to PAI in the absence of substrate/product shows the 30-Å path from the surface to the active site FAD (drawn as sticks). (c) Conformational changes in active site associated with PEG 400 binding reveal the gating mechanism. PEG 400, Phe-193, and Arg-88 are in the open conformation when PEG 400 is bound (blue) compared with the apoenzyme (gray). Arg-88 displays two conformations in the open form of PAI, both of which point away from the entering substrate.

Figures were selected by an automated process.