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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

Structures of the heme pockets of the heme Fe(II)-O2 complex (left, PDB code: 1VB6) and the heme Fe(II) complex (right, PDB code: 1V9Z) of Ec DOS-PAS-A [27,28]. The catalytic enhancement of Ec DOS by added O2 (or NO/CO) is caused by dissociation of the 6th axial ligand M95 from the heme Fe(II) complex. Dissociation of M95 releases the locked state in the heme environment, allowing catalysis to occur. The O2 molecule is represented by the orange dumbbells. Adapted from [33].
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biosensors-03-00211-f008: Structures of the heme pockets of the heme Fe(II)-O2 complex (left, PDB code: 1VB6) and the heme Fe(II) complex (right, PDB code: 1V9Z) of Ec DOS-PAS-A [27,28]. The catalytic enhancement of Ec DOS by added O2 (or NO/CO) is caused by dissociation of the 6th axial ligand M95 from the heme Fe(II) complex. Dissociation of M95 releases the locked state in the heme environment, allowing catalysis to occur. The O2 molecule is represented by the orange dumbbells. Adapted from [33].

Mentions: It has been confirmed that Ec DOS has PDE activity toward c-di-GMP and its basal PDE activity toward c-di-GMP is substantially stimulated by binding of O2 (as well as NO and CO) to the heme Fe(II) complex in the enzyme [24,25]. Furthermore, M95, the axial ligand to the 6-coordinated heme Fe(II) complex in Ec DOS, was found to play a critical role in regulating the catalytic activity toward c-di-GMP. Specifically, from a coordination chemistry point of view, upon binding of the exogenous axial ligand O2 (or NO/CO) to the heme Fe(II) complex in the wild-type (WT) protein, the internal 6th axial ligand, M95, must first dissociate from the heme plane. In the next step, the exogenous axial ligand is bound to the heme Fe(II) complex [27,28]. Thus, it would appear that the protein movement caused by dissociation of M95 from the heme iron complex pushes part of the protein on the heme distal site upward or causes it to twist, leading to catalytic enhancement via intramolecular signal transduction. This supposition was tested by examining how mutations at M95 influence catalytic activity toward c-di-GMP. For M95A and M95L mutants, in which the heme iron complex takes the 5-coordinated form because there is no axial ligand at the 6th position, basal catalytic activities were high without the external axial ligand and further addition of the exogenous ligand, O2 (or NO/CO), did not significantly enhance catalysis. Interestingly, for M95H, where His is coordinated to the heme Fe(II) complex and a 6-coordinated complex is formed, addition of external ligands induced a catalytic enhancement similar to that observed for the WT enzyme. On the basis of these findings, it was proposed that M95 is coordinated to the heme Fe(II) complex under basal conditions and suppresses the catalysis. Subsequent binding of O2 (or NO/CO) to the heme Fe(II) complex unlocks the suppression and allows catalytic enhancement (Figure 8) [27,28].


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

Shimizu T - Biosensors (Basel) (2013)

Structures of the heme pockets of the heme Fe(II)-O2 complex (left, PDB code: 1VB6) and the heme Fe(II) complex (right, PDB code: 1V9Z) of Ec DOS-PAS-A [27,28]. The catalytic enhancement of Ec DOS by added O2 (or NO/CO) is caused by dissociation of the 6th axial ligand M95 from the heme Fe(II) complex. Dissociation of M95 releases the locked state in the heme environment, allowing catalysis to occur. The O2 molecule is represented by the orange dumbbells. Adapted from [33].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

biosensors-03-00211-f008: Structures of the heme pockets of the heme Fe(II)-O2 complex (left, PDB code: 1VB6) and the heme Fe(II) complex (right, PDB code: 1V9Z) of Ec DOS-PAS-A [27,28]. The catalytic enhancement of Ec DOS by added O2 (or NO/CO) is caused by dissociation of the 6th axial ligand M95 from the heme Fe(II) complex. Dissociation of M95 releases the locked state in the heme environment, allowing catalysis to occur. The O2 molecule is represented by the orange dumbbells. Adapted from [33].
Mentions: It has been confirmed that Ec DOS has PDE activity toward c-di-GMP and its basal PDE activity toward c-di-GMP is substantially stimulated by binding of O2 (as well as NO and CO) to the heme Fe(II) complex in the enzyme [24,25]. Furthermore, M95, the axial ligand to the 6-coordinated heme Fe(II) complex in Ec DOS, was found to play a critical role in regulating the catalytic activity toward c-di-GMP. Specifically, from a coordination chemistry point of view, upon binding of the exogenous axial ligand O2 (or NO/CO) to the heme Fe(II) complex in the wild-type (WT) protein, the internal 6th axial ligand, M95, must first dissociate from the heme plane. In the next step, the exogenous axial ligand is bound to the heme Fe(II) complex [27,28]. Thus, it would appear that the protein movement caused by dissociation of M95 from the heme iron complex pushes part of the protein on the heme distal site upward or causes it to twist, leading to catalytic enhancement via intramolecular signal transduction. This supposition was tested by examining how mutations at M95 influence catalytic activity toward c-di-GMP. For M95A and M95L mutants, in which the heme iron complex takes the 5-coordinated form because there is no axial ligand at the 6th position, basal catalytic activities were high without the external axial ligand and further addition of the exogenous ligand, O2 (or NO/CO), did not significantly enhance catalysis. Interestingly, for M95H, where His is coordinated to the heme Fe(II) complex and a 6-coordinated complex is formed, addition of external ligands induced a catalytic enhancement similar to that observed for the WT enzyme. On the basis of these findings, it was proposed that M95 is coordinated to the heme Fe(II) complex under basal conditions and suppresses the catalysis. Subsequent binding of O2 (or NO/CO) to the heme Fe(II) complex unlocks the suppression and allows catalytic enhancement (Figure 8) [27,28].

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