Primary Structure Characterization of a Rhodocyclus tenuis Diheme Cytochrome c Reveals the Existence of Two Different Classes of Low-Potential Diheme Cytochromes c in Purple Phototropic Bacteria

Devreese, Bart; Brigé, Ann; Backers, Katrien; Driessche, Gonzalez Van; Meyer, Terrance E.; Cusanovich, Michael A.; Beeumen, Jozef J. Van

doi:10.1006/abbi.2000.1971

Cited by 5 publications

(3 citation statements)

References 16 publications

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“…Extended heme attachment motifs in the form of CX 3 CH or CX 4 CH occur in tetraheme cyts c 3 of sulfate-reducing bacteria [69] and in a few other cyts c [70]. In an analysis of heme conformation performed on cyts c 3 , it was discovered that hemes 2 and 4, which have extended heme attachment motifs, tend to be significantly more ruffled than hemes 1 and hemes 3 [69].…”

Section: Functional Implicationsmentioning

confidence: 99%

Influence of heme c attachment on heme conformation and potential

et al. 2018

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Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CXCH or CXCH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CXCH and CXCH variants of Hydrogenobacter thermophilus cytochrome c. In addition, a novel CXCH variant is studied. H andC NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CXCH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.

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Section: Functional Implicationsmentioning

confidence: 99%

Influence of heme c attachment on heme conformation and potential

et al. 2018

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“…The Ccm system can, at least in some organisms, mature c-type cytochromes with three or four residues between the cysteines of the heme-binding motif (e.g. Pseudomonas stutzeri cytochrome c 552 [21], cytochromes c 3 from sulfate reducing bacteria [22], and a variant of Rhodobacter sphaeroides cytochrome c 2 [23]). However, the specificity of the biogenesis system for such proteins is not clear, nor is there any evidence on possible limits for the number of "X" residues.…”

Section: Introductionmentioning

confidence: 99%

Variant c-type cytochromes as probes of the substrate specificity of the E. coli cytochrome c maturation (Ccm) apparatus

Allen

Sawyer

Ginger

et al. 2009

Biochemical Journal

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c-type cytochromes are normally characterized by covalent attachment of the iron cofactor haem to protein through two thioether bonds between the vinyl groups of the haem and the thiol groups of a CXXCH (Cys-Xaa-Xaa-Cys-His) motif. In cells, the haem attachment is an enzyme-catalysed post-translational modification. We have previously shown that co-expression of a variant of Escherichia coli cytochrome b(562) containing a CXXCH haem-binding motif with the E. coli Ccm (cytochrome c maturation) proteins resulted in homogeneous maturation of a correctly formed c-type cytochrome. In contrast, in the absence of the Ccm apparatus, the product holocytochrome was heterogeneous, the main species having haem inverted and attached through only one thioether bond. In the present study we use further variants of cytochrome b(562) to investigate the substrate specificity of the E. coli Ccm apparatus. The system can mature c-type cytochromes with CCXXCH, CCXCH, CXCCH and CXXCHC motifs, even though these are not found naturally and the extra cysteine residue might, in principle, disrupt the biogenesis proteins which must interact intricately with disulfide-bond oxidizing and reducing proteins in the E. coli periplasm. The Ccm proteins can also attach haem to motifs of the type CX(n)CH where n ranges from 2 to 6. For n=3 and 4, the haem attachment was correct and homogeneous, but for higher values of n the holocytochromes displayed oxidative addition of sulfur and/or oxygen atoms associated with the covalent haem-attachment process. The implications of our observations for the haem-attachment reaction, for genome analyses and for the substrate specificity of the Ccm system, are discussed.

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“…All species of Rhodocyclus apparently produce large amounts of the denitrifying diheme cytochrome NirB [ 43 ], which has been shown by the sequence of the protein from Rcy. tenuis DSM 109 T and DSM 111 [ 44 ] and by the fact that all of the Rhodocyclus genome sequences in the current study contain the nir B gene. However, none of these species apparently have the corresponding denitrifying genes for nitrite, nitric, or nitrous oxide reductases, and NirB apparently assumes a different role.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species

et al. 2022

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The genome sequences for Rhodocyclus purpureus DSM 168T and four strains assigned to Rhodocyclus tenuis (DSM 110, DSM 111, DSM 112, and IM 230) have been determined. One of the strains studied (IM 230) has an average nucleotide identity (ANI) of 97% to the recently reported genome of the type strain DSM 109 of Rcy. tenuis and is regarded as virtually identical at the species level. The ANI of 80% for three other strains (DSM 110, DSM 111, DSM 112) to the type strain of Rcy. tenuis points to a differentiation of these at the species level. Rcy. purpureus is equidistant from Rcy. tenuis and the new species, based on both ANI (78–80%) and complete proteome comparisons (70% AAI). Strains DSM 110, DSM 111, and DSM 112 are very closely related to each other based on ANI, whole genome, and proteome comparisons but clearly distinct from the Rcy. tenuis type strain DSM 109. In addition to the whole genome differentiation, these three strains also contain unique genetic differences in cytochrome genes and contain genes for an anaerobic cobalamin synthesis pathway that is lacking from both Rcy. tenuis and Rcy. purpureus. Based on genomic and genetic differences, these three strains should be considered to represent a new species, which is distinctly different from both Rcy. purpureus and Rcy. tenuis, for which the new name Rhodocyclus gracilis sp. nov. is proposed.

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Primary Structure Characterization of a Rhodocyclus tenuis Diheme Cytochrome c Reveals the Existence of Two Different Classes of Low-Potential Diheme Cytochromes c in Purple Phototropic Bacteria

Cited by 5 publications

References 16 publications

Influence of heme c attachment on heme conformation and potential

Influence of heme c attachment on heme conformation and potential

Variant c-type cytochromes as probes of the substrate specificity of the E. coli cytochrome c maturation (Ccm) apparatus

Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species

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