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Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases.

Jia C, Li M, Li J, Zhang J, Zhang H, Cao P, Pan X, Lu X, Chang W - Protein Cell (2014)

Bottom Line: The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production.Therefore, our results provide a structural explanation for the highly labile feature of cADO di-iron center, which we proposed to be related to its low enzymatic activity.On the basis of our structural and biochemical data, a possible catalytic process of cADO was proposed, which could aid the design of cADO with improved activity.

View Article: PubMed Central - PubMed

Affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

ABSTRACT
The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production. Cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne, is a key enzyme in that pathway. Due to its low activity, alk(a/e)ne production by cADO is an inefficient process. Previous biochemical and structural investigations of cADO have provided some information on its catalytic reaction. However, the details of its catalytic processes remain unclear. Here we report five crystal structures of cADO from the Synechococcus elongates strain PCC7942 in both its iron-free and iron-bound forms, representing different states during its catalytic process. Structural comparisons and functional enzyme assays indicate that Glu144, one of the iron-coordinating residues, plays a vital role in the catalytic reaction of cADO. Moreover, the helix where Glu144 resides exhibits two distinct conformations that correlates with the different binding states of the di-iron center in cADO structures. Therefore, our results provide a structural explanation for the highly labile feature of cADO di-iron center, which we proposed to be related to its low enzymatic activity. On the basis of our structural and biochemical data, a possible catalytic process of cADO was proposed, which could aid the design of cADO with improved activity.

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The substrate channel ofSeADO. (A) The conserved residues involved in the formation of the substrate channel are labelled. (B) The substrate channel is sealed by the hydrogen bond (shown as black dashed line) formed by two Tyr residues (Y21 and Y125) and a shell-like cover comprises of V128-D130 together with Y17, L74, and L191. The iron atoms are shown in spheres, and the substrate channel is shown as grey mesh
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Fig3: The substrate channel ofSeADO. (A) The conserved residues involved in the formation of the substrate channel are labelled. (B) The substrate channel is sealed by the hydrogen bond (shown as black dashed line) formed by two Tyr residues (Y21 and Y125) and a shell-like cover comprises of V128-D130 together with Y17, L74, and L191. The iron atoms are shown in spheres, and the substrate channel is shown as grey mesh

Mentions: In our different structures, the ligand is buried inside ADO molecule at the same location, with its hydrophobic tail pointing towards the N-terminal region. A number of aromatic and hydrophobic residues, which are highly conserved among diverse species of cADOs (Fig. 1A), form a hydrophobic channel to accommodate the non-polar ligand (Fig. 3A). Notably, whilst all these residues are provided by helices 1, 2, 3, 4 and 6, helix H5 is contributing little to the formation of the hydrophobic channel. This peculiar structural feature might explain why the ligands remain in the channel even in the absence of the di-iron cluster (Fig. 2C), despite the fact that the conformation of helix H5 is vastly different among our structures. We proposed that the hydrophobic channel is the actual substrate channel of cADO.Figure 3


Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases.

Jia C, Li M, Li J, Zhang J, Zhang H, Cao P, Pan X, Lu X, Chang W - Protein Cell (2014)

The substrate channel ofSeADO. (A) The conserved residues involved in the formation of the substrate channel are labelled. (B) The substrate channel is sealed by the hydrogen bond (shown as black dashed line) formed by two Tyr residues (Y21 and Y125) and a shell-like cover comprises of V128-D130 together with Y17, L74, and L191. The iron atoms are shown in spheres, and the substrate channel is shown as grey mesh
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4286721&req=5

Fig3: The substrate channel ofSeADO. (A) The conserved residues involved in the formation of the substrate channel are labelled. (B) The substrate channel is sealed by the hydrogen bond (shown as black dashed line) formed by two Tyr residues (Y21 and Y125) and a shell-like cover comprises of V128-D130 together with Y17, L74, and L191. The iron atoms are shown in spheres, and the substrate channel is shown as grey mesh
Mentions: In our different structures, the ligand is buried inside ADO molecule at the same location, with its hydrophobic tail pointing towards the N-terminal region. A number of aromatic and hydrophobic residues, which are highly conserved among diverse species of cADOs (Fig. 1A), form a hydrophobic channel to accommodate the non-polar ligand (Fig. 3A). Notably, whilst all these residues are provided by helices 1, 2, 3, 4 and 6, helix H5 is contributing little to the formation of the hydrophobic channel. This peculiar structural feature might explain why the ligands remain in the channel even in the absence of the di-iron cluster (Fig. 2C), despite the fact that the conformation of helix H5 is vastly different among our structures. We proposed that the hydrophobic channel is the actual substrate channel of cADO.Figure 3

Bottom Line: The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production.Therefore, our results provide a structural explanation for the highly labile feature of cADO di-iron center, which we proposed to be related to its low enzymatic activity.On the basis of our structural and biochemical data, a possible catalytic process of cADO was proposed, which could aid the design of cADO with improved activity.

View Article: PubMed Central - PubMed

Affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

ABSTRACT
The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production. Cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne, is a key enzyme in that pathway. Due to its low activity, alk(a/e)ne production by cADO is an inefficient process. Previous biochemical and structural investigations of cADO have provided some information on its catalytic reaction. However, the details of its catalytic processes remain unclear. Here we report five crystal structures of cADO from the Synechococcus elongates strain PCC7942 in both its iron-free and iron-bound forms, representing different states during its catalytic process. Structural comparisons and functional enzyme assays indicate that Glu144, one of the iron-coordinating residues, plays a vital role in the catalytic reaction of cADO. Moreover, the helix where Glu144 resides exhibits two distinct conformations that correlates with the different binding states of the di-iron center in cADO structures. Therefore, our results provide a structural explanation for the highly labile feature of cADO di-iron center, which we proposed to be related to its low enzymatic activity. On the basis of our structural and biochemical data, a possible catalytic process of cADO was proposed, which could aid the design of cADO with improved activity.

Show MeSH
Related in: MedlinePlus