Cytochrome <i>c</i>551 Is a Mediator of Electron Transfer between Copper-Containing Nitrite Reductase and Azurin in a Denitrifying Bacterium, <i>Achromobacter xylosoxidans</i>

Koteishi, Hiroyasu; Nojiri, Masaki; Nakagami, Takuya; Yamaguchi, Kazuya; Suzuki, Shinnichiro

doi:10.1246/bcsj.82.1003

Cited by 5 publications

(4 citation statements)

References 21 publications

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“…An important aspect of this topic relates to which redox partners carry out direct electron transfer to neisserial NirK. Although in vitro studies have identified both azurins (members of the cupredoxin family) and c -type heme cytochromes as electron donors to other members of the blue, copper - containing nitrite reductase (CuNIR) family [60] , [61] , only rarely have the physiological contributions been addressed in vivo . Although both N. meningitidis and N. gonorrhoeae express a lipoprotein form of azurin termed Laz, it has been reported that Laz is nonessential for growth under either aerobic or anerobic conditions (in the presence of nitrite) [62] .…”

Section: Discussionmentioning

confidence: 99%

Structural Alterations in a Component of Cytochrome c Oxidase and Molecular Evolution of Pathogenic Neisseria in Humans

et al. 2010

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Three closely related bacterial species within the genus Neisseria are of importance to human disease and health. Neisseria meningitidis is a major cause of meningitis, while Neisseria gonorrhoeae is the agent of the sexually transmitted disease gonorrhea and Neisseria lactamica is a common, harmless commensal of children. Comparative genomics have yet to yield clear insights into which factors dictate the unique host-parasite relationships exhibited by each since, as a group, they display remarkable conservation at the levels of nucleotide sequence, gene content and synteny. Here, we discovered two rare alterations in the gene encoding the CcoP protein component of cytochrome cbb 3 oxidase that are phylogenetically informative. One is a single nucleotide polymorphism resulting in CcoP truncation that acts as a molecular signature for the species N. meningitidis. We go on to show that the ancestral ccoP gene arose by a unique gene duplication and fusion event and is specifically and completely distributed within species of the genus Neisseria. Surprisingly, we found that strains engineered to express either of the two CcoP forms conditionally differed in their capacity to support nitrite-dependent, microaerobic growth mediated by NirK, a nitrite reductase. Thus, we propose that changes in CcoP domain architecture and ensuing alterations in function are key traits in successive, adaptive radiations within these metapopulations. These findings provide a dramatic example of how rare changes in core metabolic proteins can be connected to significant macroevolutionary shifts. They also show how evolutionary change at the molecular level can be linked to metabolic innovation and its reversal as well as demonstrating how genotype can be used to infer alterations of the fitness landscape within a single host.

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Section: Discussionmentioning

confidence: 99%

Structural Alterations in a Component of Cytochrome c Oxidase and Molecular Evolution of Pathogenic Neisseria in Humans

et al. 2010

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“…Each monomer of typical CuNiR contains two copper sites: Type 1 Cu (T1Cu) with a Cys–Met–His 2 ligand set and Type 2 Cu (T2Cu) with a His 3 ligand set ( 9–13 ). The T1Cu site accepts an electron from c -type cytochromes ( 14 , 15 ) or blue copper proteins ( 6 , 16 , 17 ), when CuNiR and the donor protein form a transient electron transfer (ET) complex. The received electron are transferred to the T2Cu site, the catalytic centre, through a Cys–His pathway.…”

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confidence: 99%

Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography

et al. 2016

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Serial femtosecond crystallography (SFX) has enabled the damage-free structural determination of metalloenzymes and filled the gaps of our knowledge between crystallographic and spectroscopic data. Crystallographers, however, scarcely know whether the rising technique provides truly new structural insights into mechanisms of metalloenzymes partly because of limited resolutions. Copper nitrite reductase (CuNiR), which converts nitrite to nitric oxide in denitrification, has been extensively studied by synchrotron radiation crystallography (SRX). Although catalytic Cu (Type 2 copper (T2Cu)) of CuNiR had been suspected to tolerate X-ray photoreduction, we here showed that T2Cu in the form free of nitrite is reduced and changes its coordination structure in SRX. Moreover, we determined the completely oxidized CuNiR structure at 1.43 Å resolution with SFX. Comparison between the high-resolution SFX and SRX data revealed the subtle structural change of a catalytic His residue by X-ray photoreduction. This finding, which SRX has failed to uncover, provides new insight into the reaction mechanism of CuNiR.

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“…CuNIR typically has a homotrimeric structure containing one type 1 (T1Cu) and one type 2 Cu (T2Cu) site per monomer. The T1Cu atom is coordinated by four amino acid residues (two histidine residues, cysteine and methionine) and functions as a receptor site for the electron supplied by an electron-donor protein such as c-type heme-containing cytochrome (8,9) or blue-copper proteins (10,11). The T2Cu site is a catalytic centre composed of three histidine residues and an axial ligand water molecule.…”

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Structural insights into the function of a thermostable copper-containing nitrite reductase

Fukuda¹,

Tse²,

Lintuluoto³

et al. 2013

The Journal of Biochemistry

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Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO À 2 ) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride-and formate-bound forms of wild type at 1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å resolution. The structure of C135A with nitrite displays a unique g 1 -O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wildtype CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CHO hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the g 1 -O coordination manner is proposed.

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Cytochrome c551 Is a Mediator of Electron Transfer between Copper-Containing Nitrite Reductase and Azurin in a Denitrifying Bacterium, Achromobacter xylosoxidans

Cited by 5 publications

References 21 publications

Structural Alterations in a Component of Cytochrome c Oxidase and Molecular Evolution of Pathogenic Neisseria in Humans

Structural Alterations in a Component of Cytochrome c Oxidase and Molecular Evolution of Pathogenic Neisseria in Humans

Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography

Structural insights into the function of a thermostable copper-containing nitrite reductase

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