Crystal Structure of Chlorite Dismutase, a Detoxifying Enzyme Producing Molecular Oxygen

Geus, Daniël C. de; Thomassen, E.A.J.; Hagedoorn, Peter‐Leon; Pannu, Navraj S.; Duijn, Esther van; Abrahams, Jan Pieter

doi:10.1016/j.jmb.2009.01.036

Cited by 68 publications

(166 citation statements)

References 47 publications

(49 reference statements)

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“…S1 in the supplemental material). In contrast to NwCld, all canonical Clds and all Cld-like proteins whose structures have been determined are homopentamers or homohexamers, respectively (11,12,16,22).…”

Section: Resultsmentioning

confidence: 99%

“…All previously determined subunit structures of Clds and Cld-like proteins (11,12,16,22) consist of two similar domains with a ferredoxin-like fold. Both domains are characterized by a four-stranded antiparallel ␤-sheet flanked by six ␣-helices.…”

Section: Resultsmentioning

confidence: 99%

“…Cld is a heme enzyme that, based on the published structural information, consists of five or six identical subunits (11,12,16,22). Besides its importance for bioengineering, Cld is extremely interesting from a biochemical perspective.…”

mentioning

confidence: 99%

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Unexpected Diversity of Chlorite Dismutases: a Catalytically Efficient Dimeric Enzyme from Nitrobacter winogradskyi

et al. 2011

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Chlorite dismutase (Cld) is a unique heme enzyme catalyzing the conversion of ClO 2؊ to Cl ؊ and O 2 . Cld is usually found in perchlorate-or chlorate-reducing bacteria but was also recently identified in a nitriteoxidizing bacterium of the genus Nitrospira. Here we characterized a novel Cld-like protein from the chemolithoautotrophic nitrite oxidizer Nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. Its three-dimensional (3D) crystal structure revealed a dimer of two identical subunits, which sharply contrasts with the penta-or hexameric structures of other chlorite dismutases. Despite a truncated N-terminal domain in each subunit, this novel enzyme turned out to be a highly efficient chlorite dismutase (K m ‫؍‬ 90 M; k cat ‫؍‬ 190 s ؊1 ; k cat /K m ‫؍‬ 2.1 ؋ 10 6 M ؊1 s ؊1 ), demonstrating a greater structural and phylogenetic diversity of these enzymes than was previously known. Based on comparative analyses of Cld sequences and 3D structures, signature amino acid residues that can be employed to assess whether uncharacterized Cld-like proteins may have a high chlorite-dismutating activity were identified. Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of N. winogradskyi exist in a large number of other microbes, including other nitrite oxidizers.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Unexpected Diversity of Chlorite Dismutases: a Catalytically Efficient Dimeric Enzyme from Nitrobacter winogradskyi

et al. 2011

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“…However, in most haeme proteins the Fe-proximal His represents the only covalent bond between the haeme chromophore and the protein, and stable incorporation of the prosthetic group occurs via several non-covalent interactions. These include H-bonding networks at the proximal side [54] as shown for haeme b-containing Clds [12,20,30,55].…”

Section: Discussionmentioning

confidence: 99%

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

et al. 2016

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SynopsisChlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from 'Candidatus Nitrospira defluvii' (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV-vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure-function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.

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“…Other Cld-family proteins have exhibited a similar level of discrepancy between gel filtration estimates and crystallographic measurements of oligomerization states (11,49,50). Aside from a subset of Clds having short monomer sequences (Ͻ 200 amino acids) (10) and the Cld from Azospirae oryzae, which appears to be a crystallographic hexamer but a pentamer via mass spectrometry, all Clds examined to date are pentamers in the solid state (11,51).…”

Section: Circular Dichroism Indicates Intact Secondary Structures Formentioning

confidence: 99%

The Chlorite Dismutase (HemQ) from Staphylococcus aureus Has a Redox-sensitive Heme and Is Associated with the Small Colony Variant Phenotype

Mayfield

Hammer

Kurker

et al. 2013

Journal of Biological Chemistry

112

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Crystal Structure of Chlorite Dismutase, a Detoxifying Enzyme Producing Molecular Oxygen

Cited by 68 publications

References 47 publications

Unexpected Diversity of Chlorite Dismutases: a Catalytically Efficient Dimeric Enzyme from Nitrobacter winogradskyi

Unexpected Diversity of Chlorite Dismutases: a Catalytically Efficient Dimeric Enzyme from Nitrobacter winogradskyi

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

The Chlorite Dismutase (HemQ) from Staphylococcus aureus Has a Redox-sensitive Heme and Is Associated with the Small Colony Variant Phenotype

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