関: cytochrome d group

WordNet

the 4th letter of the Roman alphabet (同)d
go `ding dong, like a bell (同)dong, dingdong
a ringing sound
(biochemistry) a class of hemoprotein whose principal biological function is electron transfer (especially in cellular respiration)

PrepTutorEJDIC

deuteriumの化学記号
〈鐘など〉‘を'ガンガン鳴らす / 〈鐘などが〉ガンガン鳴る / (鐘の)ガンガン鳴る音
(おもに人称代名詞・固有名詞(人名),thereの後で)had, wouldの短縮形 / (疑問文でwhere,what,whenの後で)didの短縮形;Where'd he go?=Where did he go?

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/08/09 10:23:39」(JST)

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Cytochrome d is a protein that belongs to the Cytochrome family (electron-transporting proteins). Concretely, it is an enzyme – a protein that catalyses a chemical reaction. Cytochrome d is also known as cytochrome/heme a₂. It is found in plenty of aerobic bacteria, especially when it has grown with a limited oxygen supply. The bacteria species in which it is more commonly found are Escherichia coli and Aerobacter aerogenes.^[1]

General functions

Ubiquinol to Ubiquinone reaction

Cytochrome d is, as other proteins of its family, a membrane-bound hemeprotein, but unlike cytochromes a and b, cytochrome D has a tetrapyrrolic chelate of iron as a prosthetic group^[2] instead of a heme A or heme B group. It is a dimeric protein, which means that is compound of two subunits (CydA^[3] and CydB^[4]). At the same time, cytochrome d is part of the cytochrome bd-I terminal oxidase which catalyse the two electron oxidation of ubiquinol. This process is an oxidative phosphorylation that oxidizes the ubiquinol-8 to ubiquinone. The chemical reaction followed by this process is:

         Ubiquinol-8 + O₂ = Ubiquinone-8 + H₂O^[5]

By a similar reaction, it also catalyses the reduction of oxygen to water, which involves 4 electrons.

Cytochrome d in protein complexes

Generally, in protein complexes, it gives an absorption band of approximately 636 nm or 638 nm, depending on the cytochrome d form. If it is oxidized, the band has a length of 636 nm, and a 638 nm length if it is reduced. It is commonly associated to certain prosthetic groups when found in multiple subunit complexes. Detecting cytochrome d as Fe(II) pyridine alkaline hemachrome is very difficult because the stability under these conditions is limited. If cytochrome d is pulled out of the protein complex and placed in ether containing from 1 to 5 % of HCl, it gives a different absorption band (603 nm, in the oxidized form).^[6]

Cytochrome d in Escherichia coli

The cytochrome d complex from E. coli is a heterodimer found in the bacterial cytoplasmic bilayer, where it develops the function of oxidase of the respiratory chain.^[7] Cytochrome d presents two subunits in this organism (I and II, abbreviated CydA and CydB), which were analyzed by genetic methods including alkaline phosphatase gene fusions. These fusions were done in vivo and in vitro, which implied the utilization of the transposon TnphoA in the in vivo method. The in vitro method consisted on a construction. In the end, 48 isolated fusions helped to determine the activities of the specific alkaline phosphatase in cells. The basis of the 2D models for each subunit was developed thanks to the data of these fusions and information from other resources. This basis also defines how these subunits fold in the E. coli membrane, specially in the inner one.^[8]

Cytochrome d in Azotobacter vinelandii

Azotobacter vinelandii is a nitrogen-fixing bacteria which is known by its high respiratory rate among aerobic organisms. Some physiological studies postulate that cytochrome d functions as a terminal oxidase in the membranes of this organism, taking part in the electron transport system. The studies characterized the different genes in the two subunits. A very extensive homology with CydA and CydB of the E. coli was found in these studies.^[9]

Cytochrome bd

Cytochrome bd is a tri-heme oxidase as it is compound by cytochromes b₅₅₈, b₅₉₅ and d. Its main function is the reduction of O₂ to H₂O. It is thought that it uses a di-heme active site, which is formed by the hemes of cytochromes b₅₉₅ and d. These two cytochromes are considered high-spin complexes, what is directly related to the electrons’ spin. While other respiratory terminal oxidases which catalyze that same reaction have a heme-copper active site and use a proton pump, cytochrome bd has an active site with iron instead of copper and need no proton pump as they can produce a proton-motion force themselves.^[10]

References

^ Cytochrome d group
^ Cytochrome d at the US National Library of Medicine Medical Subject Headings (MeSH)
^ Caulobacter crescentus CB15 Enzyme: cytochrome d ubiquinol oxidase subunit I
^ Caulobacter crescentus CB15 Enzyme: cytochrome d ubiquinol oxidase subunit II
^ Cytochrome d ubiquinol oxidase subunit 1
^ Cytochrome d group
^ Michael J. Miller, Robert B. Gennis. The Cytochrome d Compex Is a Coupling Site in the Aerobic Respiratory Chain of Escherichia coli. The Journal of Biological Chemistry Vol.260 No.26 (1985)
^ Escherichia coli K-12 substr. MG1655 Transporter: cytochrome bd-I terminal oxidase
^ Jones CW, Redfearn ER. The cytochrome system of Azotobacter vinelandii. Biochim Biophys Acta. 1967 Sep 6;143(2):340–353
^ Vitaliy B. Borisov, Michael I. Verkhovsky. Accommodation of CO in the di-heme active site of cytochrome bd terminal oxidase from Escherichia coli. Journal of Inorganic Biochemistry 118 (2013) 65–67

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English Journal

Electron transport and oxidative stress in Zymomonas mobilis respiratory mutants.

Strazdina I1, Kravale Z, Galinina N, Rutkis R, Poole RK, Kalnenieks U.Author information 1Institute of Microbiology and Biotechnology, University of Latvia, Kronvalda boulv. 4, 1586 Riga, Latvia.AbstractThe ethanol-producing bacterium Zymomonas mobilis is of great interest from a bioenergetic perspective because, although it has a very high respiratory capacity, the respiratory system does not appear to be primarily required for energy conservation. To investigate the regulation of respiratory genes and function of electron transport branches in Z. mobilis, several mutants of the common wild-type strain Zm6 (ATCC 29191) were constructed and analyzed. Mutant strains with a chloramphenicol-resistance determinant inserted in the genes encoding the cytochrome b subunit of the bc (1) complex (Zm6-cytB), subunit II of the cytochrome bd terminal oxidase (Zm6-cydB), and in the catalase gene (Zm6-kat) were constructed. The cytB and cydB mutants had low respiration capacity when cultivated anaerobically. Zm6-cydB lacked the cytochrome d absorbance at 630 nm, while Zm6-cytB had very low spectral signals of all cytochromes and low catalase activity. However, under aerobic growth conditions, the respiration capacity of the mutant cells was comparable to that of the parent strain. The catalase mutation did not affect aerobic growth, but rendered cells sensitive to hydrogen peroxide. Cytochrome c peroxidase activity could not be detected. An upregulation of several thiol-dependent oxidative stress-protective systems was observed in an aerobically growing ndh mutant deficient in type II NADH dehydrogenase (Zm6-ndh). It is concluded that the electron transport chain in Z. mobilis contains at least two electron pathways to oxygen and that one of its functions might be to prevent endogenous oxidative stress.
Archives of microbiology.Arch Microbiol.2012 Jun;194(6):461-71. doi: 10.1007/s00203-011-0785-7. Epub 2012 Jan 7.
The ethanol-producing bacterium Zymomonas mobilis is of great interest from a bioenergetic perspective because, although it has a very high respiratory capacity, the respiratory system does not appear to be primarily required for energy conservation. To investigate the regulation of respiratory gene
PMID 22228443

Sequence and transcriptional analysis of the genes responsible for curdlan biosynthesis in Agrobacterium sp. ATCC 31749 under simulated dissolved oxygen gradients conditions.

Zhang HT1, Zhan XB, Zheng ZY, Wu JR, Yu XB, Jiang Y, Lin CC.Author information 1Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.AbstractExpression at the mRNA level of ten selected genes in Agrobacterium sp. ATCC 31749 under various dissolved oxygen (DO) levels during curdlan fermentation related to electron transfer chain (ETC), tricarboxylic acid (TCA) cycle, peptidoglycan/lipopolysaccharide biosynthesis, and uridine diphosphate (UDP)-glucose biosynthesis were determined by qRT-PCR. Experiments were performed at DO levels of 30%, 50%, and 75%, as well as under low-oxygen conditions. The effect of high cell density on transcriptional response of the above genes under low oxygen was also studied. Besides cytochrome d (cyd A), the transcription levels of all the other genes were increased at higher DO and reached maximum at 50% DO. Under 75% DO, the transcriptional levels of all the genes were repressed. In addition, transcription levels of icd, sdh, cyo A, and fix N genes did not exhibit significant fluctuation with high cell density culture under low oxygen. These results suggested a mechanism for DO regulation of curdlan synthesis through regulation of transcriptional levels of ETCs, TCA, and UDP-glucose synthesis genes during curdlan fermentation. To our knowledge, this is the first report that DO concentration apparently regulates curdlan biosynthesis in Agrobacterium sp. ATCC 31749 providing essential lead for the optimization of the fermentation at the industrial scale.
Applied microbiology and biotechnology.Appl Microbiol Biotechnol.2011 Jul;91(1):163-75. doi: 10.1007/s00253-011-3243-1. Epub 2011 Apr 7.
Expression at the mRNA level of ten selected genes in Agrobacterium sp. ATCC 31749 under various dissolved oxygen (DO) levels during curdlan fermentation related to electron transfer chain (ETC), tricarboxylic acid (TCA) cycle, peptidoglycan/lipopolysaccharide biosynthesis, and uridine diphosphate (
PMID 21472535

Component identification of electron transport chains in curdlan-producing Agrobacterium sp. ATCC 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis.

Zhang H1, Setubal JC, Zhan X, Zheng Z, Yu L, Wu J, Chen D.Author information 1Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.AbstractAgrobacterium sp. ATCC 31749 (formerly named Alcaligenes faecalis var. myxogenes) is a non-pathogenic aerobic soil bacterium used in large scale biotechnological production of curdlan. However, little is known about its genomic information. DNA partial sequence of electron transport chains (ETCs) protein genes were obtained in order to understand the components of ETC and genomic-specificity in Agrobacterium sp. ATCC 31749. Degenerate primers were designed according to ETC conserved sequences in other reported species. DNA partial sequences of ETC genes in Agrobacterium sp. ATCC 31749 were cloned by the PCR method using degenerate primers. Based on comparative genomic analysis, nine electron transport elements were ascertained, including NADH ubiquinone oxidoreductase, succinate dehydrogenase complex II, complex III, cytochrome c, ubiquinone biosynthesis protein ubiB, cytochrome d terminal oxidase, cytochrome bo terminal oxidase, cytochrome cbb (3)-type terminal oxidase and cytochrome caa (3)-type terminal oxidase. Similarity and phylogenetic analyses of these genes revealed that among fully sequenced Agrobacterium species, Agrobacterium sp. ATCC 31749 is closest to Agrobacterium tumefaciens C58. Based on these results a comprehensive ETC model for Agrobacterium sp. ATCC 31749 is proposed.
Journal of industrial microbiology & biotechnology.J Ind Microbiol Biotechnol.2011 Jun;38(6):667-77. doi: 10.1007/s10295-010-0810-x. Epub 2010 Aug 22.
Agrobacterium sp. ATCC 31749 (formerly named Alcaligenes faecalis var. myxogenes) is a non-pathogenic aerobic soil bacterium used in large scale biotechnological production of curdlan. However, little is known about its genomic information. DNA partial sequence of electron transport chains (ETCs) pr
PMID 20730594