User:Cristiane Custodio Ross Matheus/Sandbox 1

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<StructureSection load='1ZB9' size='450' side='right' scene='' caption='Organic Hydroperoxide Resistance Protein (PDB code [[1ZB9]]).'>
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<StructureSection load='1ZB9' size='450' side='right' caption="'Organic Hydroperoxide Resistance Protein (PDB code [[1ZB9]])." >
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==Introduction==
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== Introduction ==
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'''Ohr''' is a thiol dependent antioxidant enzyme that belongs to the Ohr/OsmC family, present in bacteria and fungi, and which has the function of protecting these microorganisms from oxidative stress. It is evident, therefore, that this protein plays a central role in bacterial defense against oxidants from the host's reaction to infection. With the progress of studies on this compound it was found that Ohr are the essential actors in the decomposition of hydroperoxides of fatty acids and peroxynitrite, that is, it has these compounds as its main substrate, not presenting much efficiency in the decomposition of other types of oxidants. Within this context it is important to point out that although similar to peroxiredoxins the Ohr are not seen as such. Peroxiredoxins are nothing more than proteins that also have antioxidant action but have a structure both primary and tertiary, quite different from Ohr enzymes.. Another important point to be raised is the relevance of ohr studies for the creation of new drugs, since it is an enzyme whose structure is characteristic only of bacteria and fungi, not presenting similar structure in animals and plants. Some examples of pathogenic bacteria expressing Ohr proteins are Pseudomonas aeruginosa, Vibrio cholerae and Xylella fastidiosa. It is important to note that this protein varies according to the microorganism studied, having differences in its regulation and expression, and the focus of this page is the Ohr protein of Xylella Fastidiosa.
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'''Ohr''' é uma enzima antioxidante dependente de tiol que pertence à família das Ohr/OsmC, presente em bactérias e fungos, e que tem por função a proteção destes microrganismos ao estresse oxidativo. É evidente, portanto, que essa proteína tem um papel central na defesa bacteriana contra oxidantes advindos da reação do hospedeiro à infecção. Com o avanço dos estudos a respeito desse composto descobriu-se que as Ohr são os atores essenciais na decomposição de hidroperóxidos de ácidos graxos e peroxinitrito, ou seja, possui esses compostos como seu principal substrato, não apresentando muita eficiência na decomposição de outros tipos de oxidantes. Dentro desse contexto é importante salientar que apesar de semelhantes às peroxirredoxinas, as Ohr não são vistas como tal. As peroxirredoxinas nada mais são que proteínas que também possuem ação antioxidante mas que tem uma estrutura tanto primária quanto terciária, bem diferente das enzimas Ohr. Um outro ponto importante a se levantar é a relevância dos estudos das Ohr para a criação de novos fármacos, visto que é uma enzima cuja estrutura é característica apenas a bactérias e fungos, não apresentando estrutura similar em animais e plantas. Alguns exemplos de bactérias patogênicas que expressam proteínas Ohr são Pseudomonas aeruginosa, Vibrio cholerae e Xylella fastidiosa. É importante salientar que essa proteína varia de acordo com o microrganismo estudado, tendo diferenças em sua regulação e expressão, sendo o exemplo usado para essa página a proteína Ohr de Xylella fastidiosa
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==Organic Hydroperoxide Resistance Protein from Xylella fastidiosa (Ohr)==
==Organic Hydroperoxide Resistance Protein from Xylella fastidiosa (Ohr)==
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'''Xylella fastidiosa''' is a gram - negative bacterium, restricted colonizer of plant xylem, known to cause diseases in several monocotyledons and dicotyledons of great economic importance. Addressing the pathogen-host relationship, it was possible to observe that the plant releases reactive oxygen species that function as microbicide agents. Among the ROS produced are fatty acid hydroperoxides, generated from an oxidation reaction catalyzed by lipoxygenase enzymes. To defend itself from this oxidative attack Xylella produces the Enzyme Ohr. Within this topic it was observed that in a situation of increased stress there is no increase in the amount of enzyme, concluding that in this bacterium there is no regulatory mechanism as for most OM so that have the Ohr gene
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'''Xylella fastidiosa''' é uma bactéria gram negativa, colonizadora restrita do xilema de plantas, conhecida por causar doenças em diversas monocotiledôneas e dicotiledôneas de grande importância econômica. Abordando a relação patógeno-hospedeiro foi possível observar que a planta libera espécies reativas de oxigênios que funcionam como agentes microbicidas. Dentre as ROS produzidas se encontram os hidroperóxidos de ácidos graxos, gerados a partir de uma reação de oxidação catalisada pelas enzimas lipoxigenases. Para se defender desse ataque oxidativo a Xylella produz a enzima Ohr. Dentro desse tópico foi observado que em uma situação de aumento do estresse não há aumento da quantidade de enzima, concluindo-se que nessa bactéria não há um mecanismo regulatório como para a maioria dos MO que possuem o gene da Ohr.
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[[Image:OHRR_(2).png|left|494px]]<br />
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==Ohr gene regulation==
==Ohr gene regulation==
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'''OhrR''' is a transcriptional factor characterized by being a repressive protein and the main regulatory factor of the Ohr gene in most microorganisms. This protein is found on the promoter of the Ohr gene and has its structure altered when oxidized when it comes into contact with hydroperoxides of fatty acids and peroxynitrites. With the change of conformation generated by the oxidation of OhrR occurs its detachment from the promoter of the gene, making it more accessible to RNA polymerase, resulting in an overexpression of the Ohr gene. In addition to OhrR were also found in some microorganisms different regulatory means for the Ohr gene. An example is positive regulation by the alternative sigma factor, present in some microorganisms
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[[Image:Screenshot 20211212-110409~2.png|right|494px]]<br />
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==Structural features==
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Newbery et al 2007 reported the first crystal structure of OhrR from Xanthomonas campestris in Molecular Cell. This was the second structure of an OhrR protein to be submitted to the Protein Data Bank. For the structures of both reduced and oxidized OhrR, protein was overexpressed in ''E coli''. To produce crystals of the reduced form of the protein, site-directed mutagenesis was performed to mutate the reactive cysteine (Cys22) to a serine. Crystals of both unlabeled and selenomethionine-substituted reduced OhrR were generated and data collected using SAD phasing. For crystallization of the oxidized form of the protein, purified protein was treated with cumene hydroperoxide and purified via gel filtration prior to crystallization. The resulting reduced and oxidized structures were respectively named 2pex and 2pfb. Refinement of 2pex resulted in a 1.90 angstrom structure with an Rfree of 27.7% and Rwork of 23.6% and 96.7% of phi,psi angles in the most favorable regions of the Ramachandran plot. Refinement of 2pfb yielded a 1.93 angstrom structure with 96.1% of phi,psi angles in the most favorable regions of the Ramachandran plot and Rfree/Rwork value of 25.0% and 21.9% respectively. Neither of the final models included any residues in disallowed regions of the Ramachandran plot.
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Ohr presents distinct structural and biochemical characteristics when compared to cys-based mammalian peroxidases. This protein has a barrel-like structure formed by a tightly folded homodhermer, in which two β sheets of six ribbons involve two αhelix. There are two active sites in the enzyme that are located at the dye interface on opposite sides of the protein.The architecture of the Ohr catalytic site is composed of two cysteines, peroxidatic and resolution. Peroxidatic cysteine, located in one of α central helixs, has as function the direct reaction with hydroperoxides, forming a sulphenic acid. This in turn condenses with resolution cysteine to form an intramoleculardisulfide bond. In addition to the two cys amino acids there is also the presence of a catalytic arginine and a glutamate that has extreme importance in the activity of the enzyme Ohr, since they help stabilize the Cys in its thiolato state through polar interactions, increasing its nucleophilicity.The carboxylic group of catalytic glutamate guides the Guanidine group of Arginine towards Cysteine, in a configuration that seems to be ideal for the reduction of organic hydroperoxides. This described stabilization process is the so-called closed state of the catalytic triad. In the open state, there is a disruption of interactions and consequent conformational change that ends up exposing the residue to the solvent, the latter being the most conducive to the reduction of Ohr
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[[Image:OHR.png|center|494px]]<br />
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==3D structures of Ohr==
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[[Organic hydroperoxide resistance protein]]
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[[Image:2pexlabeledchains.png|left|450px]]<br />
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</StructureSection>
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==Structural features==
 
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The resulting model 2pex shows the biologically relevant dimer of the protein. Each subunit of the dimer is composed of six α-helices and 3 β-strands, as indicated below (left). The specific residues corresponding to these regions of secondary structure are as follows: α1 (residues 21–39), α2 (residues 47–58), β1(residues 62–63), α3 (residues 64–71), α4 (residues 75–87), β2 (residues 91–94), β3 (residues 104–107), α5 (residues 109–129), α6 (residues 133–151), and three-ten helices 1a (residues 13–15) and 1b (residues 17–19). The longest α-helix, α5, has a notable kink at residue G119. The dimerization interface is largely formed by three-ten helices (1a, 1b) and α1, α5, and α6 from each subunit. The extensive dimerization domain buries 5391Ų.
 
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[[Image:2pexlabeledchains.png|left|450px]]<br />
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==References==
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*ALEGRIA, Thiago Geronimo Pires. Caracterização cinética e busca de inibidores de Ohr (Organic Hydroperoxide Resistance protein) de Xylella fastidiosa. 2012. 117 f. Tese (Doutorado) - Curso de Biologia, Universidade de São Paulo, São Paulo, 2012. Disponível em: https://teses.usp.br/teses/disponiveis/41/41131/tde-23072012-160418/publico/ThiagoGeronimo_Alegria.pdf. Acesso em: 13 nov. 2021.
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==3D structures of Ohr==
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*CUSSIOL, Jose Renato Rosa. Caracterização funcional de uma nova proteína antioxidante: Ohr (Organic Hidroperoxide Resistance Protein). Vias de redução e expressão em Xylella fastidiosa. 2010. 218 f. Tese (Doutorado) - Curso de Biociências, Departamento de Biologia Evolutiva e Genética, Usp, São Paulo, 2010. Disponível em: https://www.teses.usp.br/teses/disponiveis/41/41131/tde-21072010-161740/publico/Jose_Renato_Cussiol_versao_completa.pdf. Acesso em: 13 nov. 2021.
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*NETTO, Luis.Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches. PLOS one, São Paulo, v. -, n.-,p.1-23,maio 2018.
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[[Organic hydroperoxide resistance protein]]
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*NETTO, Luis. Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle. Acs Catalysis, São Paulo, v. -, n. -, p. 6587-6602, maio 2020.

Current revision

'Organic Hydroperoxide Resistance Protein (PDB code 1ZB9).

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References

  • ALEGRIA, Thiago Geronimo Pires. Caracterização cinética e busca de inibidores de Ohr (Organic Hydroperoxide Resistance protein) de Xylella fastidiosa. 2012. 117 f. Tese (Doutorado) - Curso de Biologia, Universidade de São Paulo, São Paulo, 2012. Disponível em: https://teses.usp.br/teses/disponiveis/41/41131/tde-23072012-160418/publico/ThiagoGeronimo_Alegria.pdf. Acesso em: 13 nov. 2021.
  • CUSSIOL, Jose Renato Rosa. Caracterização funcional de uma nova proteína antioxidante: Ohr (Organic Hidroperoxide Resistance Protein). Vias de redução e expressão em Xylella fastidiosa. 2010. 218 f. Tese (Doutorado) - Curso de Biociências, Departamento de Biologia Evolutiva e Genética, Usp, São Paulo, 2010. Disponível em: https://www.teses.usp.br/teses/disponiveis/41/41131/tde-21072010-161740/publico/Jose_Renato_Cussiol_versao_completa.pdf. Acesso em: 13 nov. 2021.
  • NETTO, Luis.Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches. PLOS one, São Paulo, v. -, n.-,p.1-23,maio 2018.
  • NETTO, Luis. Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle. Acs Catalysis, São Paulo, v. -, n. -, p. 6587-6602, maio 2020.

Proteopedia Page Contributors and Editors (what is this?)

Cristiane Custodio Ross Matheus, Jaime Prilusky

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