A Globin Domain in a Neuronal Transmembrane Receptor of Caenorhabditis elegans and Ascaris suum

Tilleman, Lesley; Germani, Francesca; Henau, Sasha De; Helbo, Signe; Desmet, Filip; Berghmans, Herald; Doorslaer, Sabine Van; Hoogewijs, David; Schoofs, Liliane; Braeckman, Bart P.; Moëns, Luc; Fago, Angela; Dewilde, Sylvia

doi:10.1074/jbc.m114.576520

Cited by 8 publications

(9 citation statements)

References 95 publications

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“…These components have g values similar to those of OH – adducts of other heme proteins, such as cytochrome c peroxidase, 45 human hemoglobin, 46 horse heart myoglobin, 46 and Caenorhabditis elegans globin-33. 47 Nicoletti et al showed that at high pH hemoglobin from Thermobifida fusca forms two hydroxo complexes with different sets of g values, 48 which they explained with the OH – group being hydrogen-bonded to different extents to nearby residues. In the case of hemoglobin, the component with broader features was assigned to a strong His/OH – coordination.…”

Section: Discussionmentioning

confidence: 99%

Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis

et al. 2021

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Chlorite dismutases (Clds) are heme b -containing oxidoreductases that can decompose chlorite to chloride and molecular oxygen. They are divided in two clades that differ in oligomerization, subunit architecture, and the hydrogen-bonding network of the distal catalytic arginine, which is proposed to switch between two conformations during turnover. To understand the impact of the conformational dynamics of this basic amino acid on heme coordination, structure, and catalysis, Cld from Cyanothece sp. PCC7425 was used as a model enzyme. As typical for a clade 2 Cld, its distal arginine 127 is hydrogen-bonded to glutamine 74. The latter has been exchanged with either glutamate (Q74E) to arrest R127 in a salt bridge or valine (Q74V) that mirrors the setting in clade 1 Clds. We present the X-ray crystal structures of Q74V and Q74E and demonstrate the pH-induced changes in the environment and coordination of the heme iron by ultraviolet–visible, circular dichroism, and electron paramagnetic resonance spectroscopies as well as differential scanning calorimetry. The conformational dynamics of R127 is shown to have a significant role in heme coordination during the alkaline transition and in the thermal stability of the heme cavity, whereas its impact on the catalytic efficiency of chlorite degradation is relatively small. The findings are discussed with respect to (i) the flexible loop connecting the N-terminal and C-terminal ferredoxin-like domains, which differs in clade 1 and clade 2 Clds and carries Q74 in clade 2 proteins, and (ii) the proposed role(s) of the arginine in catalysis.

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Section: Discussionmentioning

confidence: 99%

Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis

et al. 2021

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“…Addition of dithionite to as-purified Gs GCS leads to the ferrous deoxy form with absorption maxima at 427, 561, and 532 nm, typical of LS ferrous Gbs in which the heme iron is ligated to two histidines (so-called hexa-coordination), e.g. neuroglobin [49] , cytoglobin [50] , Ce GLB6 [51] , Ce GLB26 [52] , and Ce GLB33 [24] . Of note, the Q-bands of the ferrous deoxy form appear less sharp than expected for hexa-coordination, indicating a fraction of penta-coordination which might facilitate the binding of gaseous ligands, as has been shown in vitro for Gs GCS 162 [16] .…”

Section: Resultsmentioning

confidence: 99%

“…The cDNA of Gs GCS (codons 1–300, NCBI reference protein sequence WP_010943923) was amplified by PCR using 5′-CCGCTCGAGATGCTGACCATGCAGGAAATAAAGG-3′ and 5′- GGGTACCCTAGTGGGGAGTGTAGG-3′ as forward and reverse primer, respectively. The reaction conditions applied for PCR are described elsewhere [24] . The construct was cloned into a pBAD-a vector using XhoI and HindIII restriction sites.…”

Section: Methodsmentioning

confidence: 99%

“…Although having a eukaryotic origin, these proteins coincide with the domain architecture of GCS. Both contain an N-terminally located seven transmembrane domain (TmD) to a Phe-Met-Arg-Phe (FMRF)-amide receptor and a C-terminal GD which represents either a classic or shortened globin fold for C. elegans and A. suum , respectively [24] . Another GCS containing a TmD, and the subject of this study, has been identified in the genome of the bacterium Geobacter sulfurreducens ( Gs ).…”

Section: Introductionmentioning

confidence: 99%

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Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens

Hammerschmid

Germani²,

Drusin³

et al. 2021

Computational and Structural Biotechnology Journal

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“…While the g -tensor of species OH1′ is very similar to the one found for horseradish peroxidase (HRP) [ 30 ], the parameters of OH2/OH2′ and OH3′ are more common for alkaline forms of cytochrome c peroxidase and mammalian myoglobin [ 24 , 29 , 31 ]. A high diversity of hydroxo-ligated species was found in hemoglobin of Thermobifida fusca [ 32 ] and the globin domain of the GLB-33 globin of C. elegans [ 33 ]. The Arg-232 variants (both single and double variant) do not exhibit hydroxo-ligated species.…”

Section: Resultsmentioning

confidence: 99%

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

Nys

Pfanzagl

Roefs

et al. 2021

IJMS

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Dye-decolorizing peroxidases (DyPs) have gained interest for their ability to oxidize anthraquinone-derived dyes and lignin model compounds. Spectroscopic techniques, such as electron paramagnetic resonance and optical absorption spectroscopy, provide main tools to study how the enzymatic function is linked to the heme-pocket architecture, provided the experimental conditions are carefully chosen. Here, these techniques are used to investigate the effect of active site perturbations on the structure of ferric P-class DyP from Klebsiella pneumoniae (KpDyP) and three variants of the main distal residues (D143A, R232A and D143A/R232A). Arg-232 is found to be important for maintaining the heme distal architecture and essential to facilitate an alkaline transition. The latter is promoted in absence of Asp-143. Furthermore, the non-innocent effect of the buffer choice and addition of the cryoprotectant glycerol is shown. However, while unavoidable or indiscriminate experimental conditions are pitfalls, careful comparison of the effects of different exogenous molecules on the electronic structure and spin state of the heme iron contains information about the inherent flexibility of the heme pocket. The interplay between structural flexibility, key amino acids, pH, temperature, buffer and glycerol during in vitro spectroscopic studies is discussed with respect to the poor peroxidase activity of bacterial P-class DyPs.

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A Globin Domain in a Neuronal Transmembrane Receptor of Caenorhabditis elegans and Ascaris suum

Cited by 8 publications

References 95 publications

Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis

Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis

Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

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