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The Heme-Based Oxygen-Sensor Phosphodiesterase Ec DOS (DosP): Structure-Function Relationships.

Shimizu T - Biosensors (Basel) (2013)

Bottom Line: Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain.X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding.This review summarizes the intriguing findings that have obtained for Ec DOS.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Shantou University Medical College, Shantou 515041, China. shimizu@tagen.tohoku.ac.jp.

ABSTRACT
Escherichia coli Direct Oxygen Sensor (Ec DOS, also known as Ec DosP) is a heme-based O2-sensing phosphodiesterase from Escherichia coli that catalyzes the conversion of cyclic-di-GMP to linear di-GMP. Cyclic-di-GMP is an important second messenger in bacteria, highlighting the importance of understanding structure-function relationships of Ec DOS. Ec DOS is composed of an N-terminal heme-bound O2-sensing PAS domain and a C-terminal phosphodiesterase catalytic domain. Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain. X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding. This review summarizes the intriguing findings that have obtained for Ec DOS.

No MeSH data available.


Related in: MedlinePlus

Heme redox-dependent structural changes in Ec DOS-PAS-A (PDB codes: 1V9Y and 1V9Z) [27,28]. The protein structure of the heme Fe(III) complex, a catalytically inactive form toward c-AMP, is flexible; thus the F-G loop cannot be determined, and the 6th axial ligand appears to be the hydroxide anion. In contrast, the protein structure of the heme Fe(II) complex, a catalytically active form toward c-AMP, is rigid, enabling determination of the F-G loop and identification of M95 as the 6th axial ligand. Adapted from [27].
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biosensors-03-00211-f006: Heme redox-dependent structural changes in Ec DOS-PAS-A (PDB codes: 1V9Y and 1V9Z) [27,28]. The protein structure of the heme Fe(III) complex, a catalytically inactive form toward c-AMP, is flexible; thus the F-G loop cannot be determined, and the 6th axial ligand appears to be the hydroxide anion. In contrast, the protein structure of the heme Fe(II) complex, a catalytically active form toward c-AMP, is rigid, enabling determination of the F-G loop and identification of M95 as the 6th axial ligand. Adapted from [27].

Mentions: The PDE catalytic activity of Ec DOS toward c-AMP is much lower than that toward c-di-GMP. Nevertheless, interesting findings have been obtained for Ec DOS using c-AMP as a substrate. Specifically, significant PDE activity toward c-AMP was observed for the full-length Ec DOS containing the heme Fe(II) complex (Ec DOS-heme Fe(II)), whereas activity was negligible for the full-length Ec DOS containing the heme Fe(III) complex (Ec DOS-heme Fe(III)) (Figure 5) [22], demonstrating that the heme iron redox state of Ec DOS regulates catalysis. This heme iron redox-dependent catalytic difference could be rationally explained by invoking heme redox-dependent protein structural changes [27]. Consistent with this, the crystal structure of Ec DOS-PAS-A in its inactive heme Fe(III) complex form (Ec DOS-PAS-A-heme Fe(III)) revealed a flexible protein; thus, a portion of the peptide in the heme surroundings, termed the F-G loop, and the structure of the heme distal side could not be determined. In contrast, Ec DOS-PAS-A in its active heme Fe(II) complex form (Ec DOS-PAS-A-heme Fe(II)) was shown to possess a rigid protein structure, enabling the structure of the heme distal side to be determined (Figure 6) [27,28]. These oxidation status-dependent differences in protein structure and PDE activity imply that Ec DOS is a redox-sensing PDE toward the substrate, c-AMP [29]. Note that heme-regulated catalytic regulation toward c-AMP is different from that toward c-di-GMP, as shown below.


The Heme-Based Oxygen-Sensor Phosphodiesterase Ec DOS (DosP): Structure-Function Relationships.

Shimizu T - Biosensors (Basel) (2013)

Heme redox-dependent structural changes in Ec DOS-PAS-A (PDB codes: 1V9Y and 1V9Z) [27,28]. The protein structure of the heme Fe(III) complex, a catalytically inactive form toward c-AMP, is flexible; thus the F-G loop cannot be determined, and the 6th axial ligand appears to be the hydroxide anion. In contrast, the protein structure of the heme Fe(II) complex, a catalytically active form toward c-AMP, is rigid, enabling determination of the F-G loop and identification of M95 as the 6th axial ligand. Adapted from [27].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263535&req=5

biosensors-03-00211-f006: Heme redox-dependent structural changes in Ec DOS-PAS-A (PDB codes: 1V9Y and 1V9Z) [27,28]. The protein structure of the heme Fe(III) complex, a catalytically inactive form toward c-AMP, is flexible; thus the F-G loop cannot be determined, and the 6th axial ligand appears to be the hydroxide anion. In contrast, the protein structure of the heme Fe(II) complex, a catalytically active form toward c-AMP, is rigid, enabling determination of the F-G loop and identification of M95 as the 6th axial ligand. Adapted from [27].
Mentions: The PDE catalytic activity of Ec DOS toward c-AMP is much lower than that toward c-di-GMP. Nevertheless, interesting findings have been obtained for Ec DOS using c-AMP as a substrate. Specifically, significant PDE activity toward c-AMP was observed for the full-length Ec DOS containing the heme Fe(II) complex (Ec DOS-heme Fe(II)), whereas activity was negligible for the full-length Ec DOS containing the heme Fe(III) complex (Ec DOS-heme Fe(III)) (Figure 5) [22], demonstrating that the heme iron redox state of Ec DOS regulates catalysis. This heme iron redox-dependent catalytic difference could be rationally explained by invoking heme redox-dependent protein structural changes [27]. Consistent with this, the crystal structure of Ec DOS-PAS-A in its inactive heme Fe(III) complex form (Ec DOS-PAS-A-heme Fe(III)) revealed a flexible protein; thus, a portion of the peptide in the heme surroundings, termed the F-G loop, and the structure of the heme distal side could not be determined. In contrast, Ec DOS-PAS-A in its active heme Fe(II) complex form (Ec DOS-PAS-A-heme Fe(II)) was shown to possess a rigid protein structure, enabling the structure of the heme distal side to be determined (Figure 6) [27,28]. These oxidation status-dependent differences in protein structure and PDE activity imply that Ec DOS is a redox-sensing PDE toward the substrate, c-AMP [29]. Note that heme-regulated catalytic regulation toward c-AMP is different from that toward c-di-GMP, as shown below.

Bottom Line: Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain.X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding.This review summarizes the intriguing findings that have obtained for Ec DOS.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Shantou University Medical College, Shantou 515041, China. shimizu@tagen.tohoku.ac.jp.

ABSTRACT
Escherichia coli Direct Oxygen Sensor (Ec DOS, also known as Ec DosP) is a heme-based O2-sensing phosphodiesterase from Escherichia coli that catalyzes the conversion of cyclic-di-GMP to linear di-GMP. Cyclic-di-GMP is an important second messenger in bacteria, highlighting the importance of understanding structure-function relationships of Ec DOS. Ec DOS is composed of an N-terminal heme-bound O2-sensing PAS domain and a C-terminal phosphodiesterase catalytic domain. Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain. X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding. This review summarizes the intriguing findings that have obtained for Ec DOS.

No MeSH data available.


Related in: MedlinePlus