Iron Coordination Structures of Oxygen Sensor FixL Characterized by Fe K-edge Extended X-ray Absorption Fine Structure and Resonance Raman Spectroscopy

Miyatake, Hideyuki; Mukai, Masanori; Adachi, Shin‐ichi; Nakamura, H.; Tamura, Koji; Iizuka, Tetsutarō; Shiro, Yoshitsugu; Strange, R.W.; Hasnain, S. Samar

doi:10.1074/jbc.274.33.23176

Cited by 58 publications

(56 citation statements)

References 51 publications

(59 reference statements)

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“…As the crystal structure of BjFixL-CO suggests that bound CO is not H-bonded [41], it is reasonable to suggest that the frequency difference is attributable to less off-axis distortion of the FeCO moiety in the heme domain-CO complexes. A subsequent report of the corresponding v Fe-CO and v C-O frequencies for SmFixLH-CO and SmFixLT-CO revealed kinase-dependent shifts that are also consistent with increased backbonding in SmFixLH-CO [50]. The same report provided evidence from solution EXAFS measurements indicating that \FeCO is indeed smaller when the kinase is present (154°versus 171°).…”

Section: Unique Redox Chemistry Of Fixlsupporting

confidence: 57%

“…One EXAFS study has been reported for a series of heme ligand adducts of the (SmFixLT) 2 (SmFixJ) 2 complex [50]. The results of these experiments revealed two interesting relationships.…”

Section: Solution Studies Of Equilibrium Structurementioning

confidence: 84%

“…While conformational strain on the proximal Fe-ImH bond likely contributes to the relatively low ligand association rates and stabilities of the corresponding ligand complexes, the insensitivity of its stretching frequency suggests that it does not account for the negative influence of the kinase domain on the ligand binding rates. This negative control has been suggested to derive from influence of the kinase on structure and/or dynamics in the distal heme pocket [35,50].…”

Section: Coordination Environmentmentioning

confidence: 97%

“…Thus the frequencies of these vibrations can be used as diagnostic probes of the distal heme environment because of their sensitivity to the nature of nonbonded interactions between bound CO and the distal heme pocket. The v Fe-CO and v C-O frequencies (v Fe-CO = 498 cm À1 , v C-O = 1962 cm À1 ) from solution rR studies of SmFixLT-CO show that it exhibits less distal H-bond donation to bound CO than does MbCO [50].…”

Section: Unique Redox Chemistry Of Fixlmentioning

confidence: 98%

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Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins

Rodgers

Lukat-Rodgers

2005

Journal of Inorganic Biochemistry

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Section: Unique Redox Chemistry Of Fixlsupporting

confidence: 57%

“…One EXAFS study has been reported for a series of heme ligand adducts of the (SmFixLT) 2 (SmFixJ) 2 complex [50]. The results of these experiments revealed two interesting relationships.…”

Section: Solution Studies Of Equilibrium Structurementioning

confidence: 84%

Section: Coordination Environmentmentioning

confidence: 97%

Section: Unique Redox Chemistry Of Fixlmentioning

confidence: 98%

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Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins

Rodgers

Lukat-Rodgers

2005

Journal of Inorganic Biochemistry

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“…Moreover, haem ligand switching induces conformational changes in the FG loop region and movement of two subunits. These structural changes may play critical roles in catalytic regulation of the PDE domain [4].Structures of the haem-bound PAS domain have been reported under various conditions, and structure-function relationships are well documented [8][9][10][11][12][13][14]. FixL is an oxygen sensor enzyme with a haem-bound PAS domain.…”

mentioning

confidence: 99%

Critical roles of Asp40 at the haem proximal side of haem‐regulated phosphodiesterase from Escherichia coli in redox potential, auto‐oxidation and catalytic control

Watanabe

Kurokawa

Yoshimura-Suzuki

et al. 2004

European Journal of Biochemistry

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In haem-regulated phosphodiesterase (PDE) from Escherichia coli (Ec DOS), haem is bound to the PAS domain, and the redox state of the haem iron regulates catalysis by the PDE domain. We generated mutants of Asp40, which forms a hydrogen bond with His77 (a proximal haem axial ligand) via two water molecules, and a salt bridge with Arg85 at the protein surface. The redox potential of haem was markedly increased from 67 mV vs. the standard hydrogen electrode in the wild-type enzyme to 95 mV and 114 mV in the Ala and Asn mutants, respectively. Additionally, the auto-oxidation rate of Ec DOS PAS was significantly increased from 0.0053 to 0.051 and 0.033 min )1 , respectively. Interestingly, the catalytic activities of the Asp40 mutants were abolished completely. Thus, Asp40 appears to play a critical role in the electronic structure of the haem iron and redox-dependent catalytic control of the PDE domain. In this report, we discuss the mechanism of catalytic control of Ec DOS, based on the physico-chemical characteristics of the Asp40 mutants.Keywords: auto-oxidation; haem axial ligand; haem sensor; phosphodiesterase; redox potential.Haem-regulated phosphodiesterase (PDE) from Escherichia coli (Ec DOS) is a haem sensor enzyme composed of two functional domains: an N-terminal haem-bound sensor domain and a C-terminal PDE catalytic domain [1,2]. Catalysis by this enzyme is regulated by the haem redox state in that PDE is functional in the Fe(II) haembound enzyme, but not the Fe(III) haem-bound enzyme [2,3]. The crystal structure of the haem-bound domain revealed a typical PAS structure [4,5]. PAS proteins display a characteristic three-dimensional structure with a glove-like fold consisting of five juxtaposed b-sheets and flanking a-helices [6][7][8][9]. The characteristic three-dimensional structure of the PAS domain is commonly used for discussing the signal transduction mechanism of numerical signal transducing enzymes [6][7][8][9]. The crystal structures of both the Fe(II) and Fe(III) forms of the isolated haem-bound PAS domain (Ec DOS PAS) disclose that haem axial ligand switching from His77/ hydroxide anion to the His77/Met95 ligand pair occurs upon haem reduction. Moreover, haem ligand switching induces conformational changes in the FG loop region and movement of two subunits. These structural changes may play critical roles in catalytic regulation of the PDE domain [4].Structures of the haem-bound PAS domain have been reported under various conditions, and structure-function relationships are well documented [8][9][10][11][12][13][14]. FixL is an oxygen sensor enzyme with a haem-bound PAS domain. Specifically, O 2 association/dissociation to/from the haem switches off/on catalysis [8,9]. Global structural changes at the haem distal side are induced upon O 2 binding to FixL, and these changes contribute significantly to intramolecular signal transduction [9][10][11]. For Ec DOS, site-directed mutations at Met95, the axial ligand at the distal side in the Fe(II) complex, induced significant changes in the redox p...

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Symbiotic Nitrogen Fixation

Kouchi

2011

Plant Metabolism and Biotechnology

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Nitrogen for all living organisms ultimately comes from atmospheric dinitrogen (N 2 ). Biological nitrogen fixation is a reaction whereby N 2 is reduced to ammonium (NH 3 ) by a special enzymatic system, of which the primary enzyme is the nitrogenase complex. The nitrogenase system is found in various prokaryotes (diazotrophic bacteria or diazotrophs). They can be grouped into two categories: one is the group of free-living nitrogen fixers which inhabit the soil, fresh water and seawater, and the other is a group of bacteria that exhibits a highly efficient nitrogen fixation system in endosymbiotic association with plants. Symbiotic nitrogen fixation in legumes is the prominent representative of the second group. Legume plants form root nodules by symbiosis with a group of soil bacteria collectively termed Rhizobium, in which endosymbiotic rhizobia are capable of fixing N 2 . Nitrogen fixation by the legume-Rhizobium symbiosis accounts for more than 50% of biological nitrogen fixation and has a critical importance in agriculture. Some kinds of symbiotic nitrogen fixers are able to fix nitrogen in their free-living state, and such free-living nitrogen fixing bacteria can reside (not intracellularly) inside the tissues of higher plants. For example, some kinds of endophytic bacteria, which inhabit the intercellular space and/or the vascular cylinders of plants, fix N 2 , and are thought to contribute nitrogen nutrition to these plants. In addition, various free-living nitrogen-fixing bacteria have been identified from the rhizosphere of many plants, and make a loose symbiotic association with those plants. Representatives of nitrogen-fixing microorganisms are shown in Table 3.1.Plant Metabolism and Biotechnology, First Edition. Edited by Hiroshi Ashihara, Alan Crozier, and Atsushi Komamine.

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Iron Coordination Structures of Oxygen Sensor FixL Characterized by Fe K-edge Extended X-ray Absorption Fine Structure and Resonance Raman Spectroscopy

Cited by 58 publications

References 51 publications

Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins

Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins

Critical roles of Asp40 at the haem proximal side of haem‐regulated phosphodiesterase from Escherichia coli in redox potential, auto‐oxidation and catalytic control

Symbiotic Nitrogen Fixation

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