Introduction of water into the heme distal side by Leu65 mutations of an oxygen sensor, YddV, generates verdoheme and carbon monoxide, exerting the heme oxygenase reaction

Stráňava, Martin; Martínková, Markéta; Stiborová, Marie; Man, Petr; Kitanishi, Kenichi; Muchová, Lucie; Vı́tek, Libor; Martínek, Václav; Shimizu, Tôru

doi:10.1016/j.jinorgbio.2014.06.010

Cited by 13 publications

(13 citation statements)

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“…Redox‐ and coordination state‐dependent changes in the flexibility of the heme active site were also observed for the globin domain of the oxygen sensor protein YddV. Although these changes did not appear to correlate with this enzyme's activity, incorporation of an external water molecule into the heme‐containing globin domain of YddV appeared to increase its rigidity.…”

Section: Discussionmentioning

confidence: 95%

“…Spectroscopic studies have suggested that the Tyr43 residue of YddV interacts with O 2 molecules when they bind to its heme Fe(II) complex . In addition, there is evidence that the Leu65 residue prevents water molecules from accessing the distal coordination site of the heme moiety, and thereby inhibits rapid autoxidation of the heme Fe(II)–O 2 complex or even inhibits heme degradation resulting in formation of verdoheme and carbon monoxide .…”

Section: Introductionmentioning

confidence: 99%

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Pressure effects reveal that changes in the redox states of the heme iron complexes in the sensor domains of two heme‐based oxygen sensor proteins, EcDOS and YddV, have profound effects on their flexibility

et al. 2014

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The catalytic activity of a heme‐based oxygen sensor phosphodiesterase from Escherichia coli (EcDOS) towards cyclic diGMP is regulated by the redox state of the heme iron complex in the enzyme's sensing domain and the association of external ligands with the iron center. Specifically, the Fe(II) complex is more active towards cyclic diGMP than the Fe(III) complex, and its activity is further enhanced by O2 or CO binding. In order to determine how the redox state and coordination of the heme iron atom regulate the catalytic activity of EcDOS, we investigated the flexibility of its isolated N‐terminal heme‐binding domain (EcDOS‐heme) by monitoring its spectral properties at various hydrostatic pressures. The most active form of the heme‐containing domain, i.e. the Fe(II)–CO complex, was found to be the least flexible. Conversely, the oxidized Fe(III) forms of EcDOS‐heme and its mutants had relatively high flexibilities, which appeared to be linked to the low catalytic activity of the corresponding intact enzymes. These findings corroborate the suggestion, made on the basis of crystallographic data, that there is an inverse relationship between the flexibility of the heme‐containing domain of EcDOS and its catalytic activity. The Fe(II)–CO form of the heme domain of a second heme‐based oxygen sensor, diguanylate cyclase (YddV), was also found to be quite rigid. Interestingly, the incorporation of a water molecule into the heme complex of YddV caused by mutation of the Leu65 residue reduced the flexibility of this heme domain. Conversely, mutation of the Tyr43 residue increased its flexibility.

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Section: Discussionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Pressure effects reveal that changes in the redox states of the heme iron complexes in the sensor domains of two heme‐based oxygen sensor proteins, EcDOS and YddV, have profound effects on their flexibility

et al. 2014

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“…Cloning, site-directed mutagenesis, overexpression in E. coli and purification of YddV-heme were performed as previously described. 3,19,20 WT and Y43F, Y43L, Y43W, L65M, and L65T mutants of YddV-heme were prepared as described below. In brief, E. coli BL21 (DE3) (Stratagene, Novagen) was transformed with an appropriate plasmid (pET28a(+)/YddV-heme-Histag), plated on LB agar containing kanamycin (50 mg mL À1 ) and incubated at 37 1C overnight.…”

Section: Overexpression and Protein Purificationmentioning

confidence: 99%

“…3 At the distal site, it has been demonstrated that the conserved residues L65 and Y43 are important for the binding and stabilization of the heme Fe(II)-O 2 complex. 3,19,20 Extensive pH studies on L65 mutant proteins have revealed the presence of a H 2 O molecule as the sixth axial ligand, which is converted to OH À at alkaline pH, and the formation of a sixcoordinate low-spin species. 19 RR Soret excitation experiments on wild-type and Y43F mutant proteins have been reported.…”

Section: Introductionmentioning

confidence: 99%

Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy

Pavlou

Martínková

Shimizu

et al. 2015

Phys. Chem. Chem. Phys.

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YddV is a newly discovered signal transducer heme protein that recognizes O2 and CO. Structural differences in the ligand-bound heme complex in YddV reflect variations in catalytic regulation by O2 and CO. Time-resolved step-scan (TRS(2)) FTIR studies of the wild type and of the important in oxygen recognition and stability of the heme Fe(II)-O2 complex L65M, L65T, Y43A, Y43F and Y43W mutants were performed to determine the site-specific protein dynamics following carbon monoxide (CO) photodissociation. These mutations were designed to perturb the electrostatic field near the iron-bound gaseous ligand (CO) and also to allow us to investigate the communication pathway between the distal residues of the protein and heme. TRS(2)-FTIR spectra of YddV-heme-CO show that the heme propionates are in protonated and deprotonated states. Moreover, the rate of decay of the vibrations of amide I is on a time scale that coincides with the rate of rebinding of CO, which suggests that there is coupling between ligation dynamics in the distal heme environment and (i) relaxation of the protein backbone and (ii) the environment sensed by the heme propionates. The fast recombination rates in L65M, L65T and Y43W imply a significant role of L65 and Y43 in controlling the ligand dynamics. The implications of these results with respect to the role of the heme propionates and the charged or proton-donating residues in the distal pocket, which are crucial for stabilizing bound gaseous ligands, are discussed.

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“…Based on in vitro reactivity, however, it is possible that GCSs could function in CO ( 76 , 78 , 79 ) or HCN sensing ( 76 , 78 , 79 ), although a physiological role for these latter functions has not been established. Coordination of O 2 in the binding pocket by Fe(II)-heme and distal threonine and tyrosine residues ( 80 ) causes the α-helices to rearrange ( 75 , 76 , 78 , 79 , 81 ), and this change is transmitted to the adjacent output domain through a coiled-coil region at the C terminus of the GCS ( 77 ).…”

Section: Modular Sensory and Receiver Domains Found In Dgcs And C-di-...mentioning

confidence: 99%

Sensory Perception in Bacterial Cyclic Diguanylate Signal Transduction

et al. 2022

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Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviours in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information-processing via c-di-GMP signal transduction is not only fundamental to bacterial survival in dynamic environments, but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.

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Introduction of water into the heme distal side by Leu65 mutations of an oxygen sensor, YddV, generates verdoheme and carbon monoxide, exerting the heme oxygenase reaction

Cited by 13 publications

References 40 publications

Pressure effects reveal that changes in the redox states of the heme iron complexes in the sensor domains of two heme‐based oxygen sensor proteins, EcDOS and YddV, have profound effects on their flexibility

Pressure effects reveal that changes in the redox states of the heme iron complexes in the sensor domains of two heme‐based oxygen sensor proteins, EcDOS and YddV, have profound effects on their flexibility

Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy

Sensory Perception in Bacterial Cyclic Diguanylate Signal Transduction

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