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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 coordination of di-iron center in the structures of Y122F (A), WT1 (B), F86YF87Y (C), and WT-HP (D). Iron atoms are shown in spheres, the coordinating residues and ligand are shown in sticks. The structures of Y122F, WT1, F86YF87Y, and WT-HP are shown in yellow, cyan, orange, and magenta, respectively
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Fig5: The coordination of di-iron center in the structures of Y122F (A), WT1 (B), F86YF87Y (C), and WT-HP (D). Iron atoms are shown in spheres, the coordinating residues and ligand are shown in sticks. The structures of Y122F, WT1, F86YF87Y, and WT-HP are shown in yellow, cyan, orange, and magenta, respectively

Mentions: In order to test the effects of residues surrounding the di-iron center and substrate channel on cADO’s catalytic activity, we constructed several mutant forms by site-directed mutagenesis, and then determined the iron content and enzymatic activity of these mutants relative to the wild type (Fig. 4 and Table 2). In addition, the crystal structures of specific mutants were solved. Intriguingly, two mutant structures (Y122F and F86YF87Y) and three wild type structures exhibit different conformations at their active site (Fig. 5) which may represent different states of the enzyme in the reaction cycle. Based on the character of the ligand molecules and the coordination mode of the iron atoms, we assign our five structures in a different states in ADO catalytic reaction below.Figure 5


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 coordination of di-iron center in the structures of Y122F (A), WT1 (B), F86YF87Y (C), and WT-HP (D). Iron atoms are shown in spheres, the coordinating residues and ligand are shown in sticks. The structures of Y122F, WT1, F86YF87Y, and WT-HP are shown in yellow, cyan, orange, and magenta, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: The coordination of di-iron center in the structures of Y122F (A), WT1 (B), F86YF87Y (C), and WT-HP (D). Iron atoms are shown in spheres, the coordinating residues and ligand are shown in sticks. The structures of Y122F, WT1, F86YF87Y, and WT-HP are shown in yellow, cyan, orange, and magenta, respectively
Mentions: In order to test the effects of residues surrounding the di-iron center and substrate channel on cADO’s catalytic activity, we constructed several mutant forms by site-directed mutagenesis, and then determined the iron content and enzymatic activity of these mutants relative to the wild type (Fig. 4 and Table 2). In addition, the crystal structures of specific mutants were solved. Intriguingly, two mutant structures (Y122F and F86YF87Y) and three wild type structures exhibit different conformations at their active site (Fig. 5) which may represent different states of the enzyme in the reaction cycle. Based on the character of the ligand molecules and the coordination mode of the iron atoms, we assign our five structures in a different states in ADO catalytic reaction below.Figure 5

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