One fold, two functions: cytochrome P460 and cytochrome <i>c</i>′-β from the methanotroph <i>Methylococcus capsulatus</i> (Bath)

Adams, Hannah R.; Krewson, Callie; Vardanega, Jenny E.; Fujii, Sotaro; Moreno, Tadeo; Chicano, Chicano; Sambongi, Yoshihiro; Svistunenko, Dimitri A.; Paps, Jordi; Andrew, Colin R.; Hough, Michael A.

doi:10.1039/c8sc05210g

Cited by 14 publications

(36 citation statements)

References 54 publications

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“…The ferrous wild-type TTCP-exhibited an absorbance maximum at 433 nm, as observed for MCCP- (Adams et al, 2019). This peak shifted to 419 and 395 nm in the presence of CO and NO, respectively (Fig.…”

Section: Preparation Of Ttcp-b and Spectroscopic Featuressupporting

confidence: 55%

“…3c), indicating cooperative denaturation. Wild-type TTCP-exhibited a T m of 116.9 AE 0.1 C (a mean value for three independent experiments with the standard deviation), which was higher than that of MCCP- (Adams et al, 2019).…”

Section: Thermal Stability Of Ttcp-b and Its Variantmentioning

confidence: 86%

“…The structure of TTCP-was determined by the molecular replacement method with Phaser as included in the Phenix suite (McCoy et al, 2007;Liebschner et al, 2019) using the crystal structure of MCCP-(PDB entry 6hih; Adams et al, 2019) as a search model. Structural refinement, manual model building and addition of water molecules were carried out using phenix.refine and Coot (Emsley et al, 2010;Adams et al, 2010).…”

Section: Molecular Replacement Refinement and Structural Analysismentioning

confidence: 99%

“…Homodimeric cytochrome c 0 -has an antiparallel -sheet structure (Elmore et al, 2007;Adams et al, 2019), in contrast to cytochrome c 0 -, which has a four-helix bundle structure (Ambler, 1991;Shibata et al, 1998;Hough & Andrew, 2015;Suka et al, 2019). Cytochrome c 0 -from the nitrifying and ISSN 2053-230X methanotrophic Methylococcus capsulatus (MCCP-) shares a similar and unique fold and occurs together with cytochrome P460 from the same source bacterium, which has been shown to oxidize hydroxylamine as part of nitrification (Pearson et al, 2007;Adams et al, 2019). Cytochrome c 0 -and cytochrome P460 differ in that the former lacks the additional protein-toheme cross-link and polar pocket that are observed in the latter.…”

Section: Introductionmentioning

confidence: 99%

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Crystal structure of thermally stable homodimeric cytochrome c′-β from Thermus thermophilus

Yoshimi

Fujii

Oki

et al. 2022

Acta Crystallogr F Struct Biol Commun

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Cytochrome c′-β is a heme protein that belongs to the cytochrome P460 family and consists of homodimeric subunits with a predominantly antiparallel β-sheet fold. Here, the crystal structure of cytochrome c′-β from the thermophilic Thermus thermophilus (TTCP-β) is reported at 1.74 Å resolution. TTCP-β has a typical antiparallel β-sheet fold similar to that of cytochrome c′-β from the moderately thermophilic Methylococcus capsulatus (MCCP-β). The phenylalanine cap structure around the distal side of the heme is also similar in TTCP-β and MCCP-β, indicating that both proteins similarly bind nitric oxide and carbon monoxide, as observed spectroscopically. Notably, TTCP-β exhibits a denaturation temperature of 117°C, which is higher than that of MCCP-β. Mutational analysis reveals that the increased homodimeric interface area of TTCP-β contributes to its high thermal stability. Furthermore, 14 proline residues, which are mostly located in the TTCP-β loop regions, possibly contribute to the rigid loop structure compared with MCCP-β, which has only six proline residues. These findings, together with those from phylogenetic analysis, suggest that the structures of Thermus cytochromes c′-β, including TTCP-β, are optimized for function under the high-temperature conditions in which the source organisms live.

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Section: Preparation Of Ttcp-b and Spectroscopic Featuressupporting

confidence: 55%

Section: Thermal Stability Of Ttcp-b and Its Variantmentioning

confidence: 86%

Section: Molecular Replacement Refinement and Structural Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Crystal structure of thermally stable homodimeric cytochrome c′-β from Thermus thermophilus

Yoshimi

Fujii

Oki

et al. 2022

Acta Crystallogr F Struct Biol Commun

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“…The genomes also encode nitric oxide reductases CytS and sNOR [15]. The role of the CytS is likely to mitigate toxicity of nitric oxide that escapes from incomplete hydroxylamine oxidation to nitrite by HAO under fully oxic conditions [78,79], although it is hypothesized that CytS might have a possible role as a nitric oxide-binding protein instead [80]. The expression products of these genes account for the abilities of all the strains to release nitrous oxide when the cultures are maintained in ammonium minimal media [81].…”

Section: Nitrogen Metabolism Inventorymentioning

confidence: 99%

High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution

2020

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The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.

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Conformational rigidity of cytochrome c'-α from a thermophile is associated with slow NO binding

Fujii,

Wilson,

Adams

et al. 2024

Biophysical Journal

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One fold, two functions: cytochrome P460 and cytochrome c′-β from the methanotroph Methylococcus capsulatus (Bath)

Abstract: Structural and spectroscopic characterisation of cytochrome c′-β and cytochrome P460 from M. capsulatus (Bath) reveals highly similar protein folds but very different heme pockets, providing functional insights.

Cited by 14 publications

References 54 publications

Crystal structure of thermally stable homodimeric cytochrome c′-β from Thermus thermophilus

Crystal structure of thermally stable homodimeric cytochrome c′-β from Thermus thermophilus

High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution

Conformational rigidity of cytochrome c'-α from a thermophile is associated with slow NO binding

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