Phylogenetic distribution and structural analyses of cyanobacterial glutaredoxins (Grxs).
Identifieur interne : 000033 ( Main/Exploration ); précédent : 000032; suivant : 000034Phylogenetic distribution and structural analyses of cyanobacterial glutaredoxins (Grxs).
Auteurs : Soumila Mondal [Inde] ; Vinod Kumar [Inde] ; Shailendra P. Singh [Inde]Source :
- Computational biology and chemistry [ 1476-928X ] ; 2020.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Biologie informatique (MeSH), Cyanobactéries (composition chimique), Domaine catalytique (MeSH), Expression des gènes (effets des radiations), Glutarédoxines (classification), Glutarédoxines (composition chimique), Glutarédoxines (métabolisme), Glutathion (métabolisme), Liaison aux protéines (MeSH), Liaison hydrogène (MeSH), Lumière (MeSH), Phylogenèse (MeSH), Simulation de docking moléculaire (MeSH), Structure secondaire des protéines (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- composition chimique : Cyanobactéries, Glutarédoxines.
- effets des radiations : Expression des gènes.
- métabolisme : Glutarédoxines, Glutathion.
- Alignement de séquences, Biologie informatique, Domaine catalytique, Liaison aux protéines, Liaison hydrogène, Lumière, Phylogenèse, Simulation de docking moléculaire, Structure secondaire des protéines, Séquence d'acides aminés.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Catalytic Domain (MeSH), Computational Biology (MeSH), Cyanobacteria (chemistry), Gene Expression (radiation effects), Glutaredoxins (chemistry), Glutaredoxins (classification), Glutaredoxins (metabolism), Glutathione (metabolism), Hydrogen Bonding (MeSH), Light (MeSH), Molecular Docking Simulation (MeSH), Phylogeny (MeSH), Protein Binding (MeSH), Protein Structure, Secondary (MeSH), Sequence Alignment (MeSH).
- MESH :
- chemical , chemistry : Glutaredoxins.
- chemistry : Cyanobacteria.
- chemical , classification : Glutaredoxins.
- chemical , metabolism : Glutaredoxins, Glutathione.
- radiation effects : Gene Expression.
- Amino Acid Sequence, Catalytic Domain, Computational Biology, Hydrogen Bonding, Light, Molecular Docking Simulation, Phylogeny, Protein Binding, Protein Structure, Secondary, Sequence Alignment.
Abstract
Glutaredoxins (Grxs), the oxidoreductase proteins, are involved in several cellular processes, including maintenance of cellular redox potential and iron-sulfur homeostasis. The analysis of 503 amino acid sequences from 167 cyanobacterial species led to the identification of four classes of cyanobacterial Grxs, i.e., class I, II, V, and VI Grxs. Class III and IV Grxs were absent in cyanobacteria. Class I and II Grxs are single module oxidoreductase while class V and VI Grxs are multimodular proteins having additional modules at their C-terminal and N-terminal end, respectively. Furthermore, class VI Grxs were exclusively present in marine cyanobacteria. We also report the identification of class VI Grxs with two novel active site motif compositions. Detailed phylogenetic analysis of all four classes of Grxs revealed the presence of several subgroups within each class of Grx having variable dithiol and/or monothiol catalytic active site motif and putative glutathione binding sites. However, class II Grxs possess CGFS-type highly conserved monothiol catalytic active site motif. Sequence analysis confirmed the highly diverse nature of Grx proteins in terms of their amino acid composition; though, sequence diversity does not affect the overall 3D structure of cyanobacterial Grxs. The active site residues and putative GSH binding residues are uncharged amino acids which are present on the surface of the protein. Additionally, the presence of hydrophilic residues at the surface of Grxs confirms their solubility. Protein-ligand interaction analysis identified novel glutathione binding sites on Grxs. Regulation of Grxs encoding genes expression by light quality and quantity as well as salinity suggests their role in determining the fitness of organisms under abiotic factors.
DOI: 10.1016/j.compbiolchem.2019.107141
PubMed: 31839562
Affiliations:
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The analysis of 503 amino acid sequences from 167 cyanobacterial species led to the identification of four classes of cyanobacterial Grxs, i.e., class I, II, V, and VI Grxs. Class III and IV Grxs were absent in cyanobacteria. Class I and II Grxs are single module oxidoreductase while class V and VI Grxs are multimodular proteins having additional modules at their C-terminal and N-terminal end, respectively. Furthermore, class VI Grxs were exclusively present in marine cyanobacteria. We also report the identification of class VI Grxs with two novel active site motif compositions. Detailed phylogenetic analysis of all four classes of Grxs revealed the presence of several subgroups within each class of Grx having variable dithiol and/or monothiol catalytic active site motif and putative glutathione binding sites. However, class II Grxs possess CGFS-type highly conserved monothiol catalytic active site motif. Sequence analysis confirmed the highly diverse nature of Grx proteins in terms of their amino acid composition; though, sequence diversity does not affect the overall 3D structure of cyanobacterial Grxs. The active site residues and putative GSH binding residues are uncharged amino acids which are present on the surface of the protein. Additionally, the presence of hydrophilic residues at the surface of Grxs confirms their solubility. Protein-ligand interaction analysis identified novel glutathione binding sites on Grxs. Regulation of Grxs encoding genes expression by light quality and quantity as well as salinity suggests their role in determining the fitness of organisms under abiotic factors.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31839562</PMID><DateCompleted><Year>2020</Year><Month>02</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1476-928X</ISSN><JournalIssue CitedMedium="Internet"><Volume>84</Volume><PubDate><Year>2020</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Computational biology and chemistry</Title><ISOAbbreviation>Comput Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Phylogenetic distribution and structural analyses of cyanobacterial glutaredoxins (Grxs).</ArticleTitle><Pagination><MedlinePgn>107141</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1476-9271(19)30419-0</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.compbiolchem.2019.107141</ELocationID><Abstract><AbstractText>Glutaredoxins (Grxs), the oxidoreductase proteins, are involved in several cellular processes, including maintenance of cellular redox potential and iron-sulfur homeostasis. The analysis of 503 amino acid sequences from 167 cyanobacterial species led to the identification of four classes of cyanobacterial Grxs, i.e., class I, II, V, and VI Grxs. Class III and IV Grxs were absent in cyanobacteria. Class I and II Grxs are single module oxidoreductase while class V and VI Grxs are multimodular proteins having additional modules at their C-terminal and N-terminal end, respectively. Furthermore, class VI Grxs were exclusively present in marine cyanobacteria. We also report the identification of class VI Grxs with two novel active site motif compositions. Detailed phylogenetic analysis of all four classes of Grxs revealed the presence of several subgroups within each class of Grx having variable dithiol and/or monothiol catalytic active site motif and putative glutathione binding sites. However, class II Grxs possess CGFS-type highly conserved monothiol catalytic active site motif. Sequence analysis confirmed the highly diverse nature of Grx proteins in terms of their amino acid composition; though, sequence diversity does not affect the overall 3D structure of cyanobacterial Grxs. The active site residues and putative GSH binding residues are uncharged amino acids which are present on the surface of the protein. Additionally, the presence of hydrophilic residues at the surface of Grxs confirms their solubility. Protein-ligand interaction analysis identified novel glutathione binding sites on Grxs. Regulation of Grxs encoding genes expression by light quality and quantity as well as salinity suggests their role in determining the fitness of organisms under abiotic factors.</AbstractText><CopyrightInformation>Copyright © 2019 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mondal</LastName><ForeName>Soumila</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centre of Advanced Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kumar</LastName><ForeName>Vinod</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Centre of Advanced Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Shailendra P</ForeName><Initials>SP</Initials><AffiliationInfo><Affiliation>Centre of Advanced Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, UP, India. Electronic address: spsingh@bhu.ac.in.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>12</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Comput Biol Chem</MedlineTA><NlmUniqueID>101157394</NlmUniqueID><ISSNLinking>1476-9271</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D054477">Glutaredoxins</NameOfSubstance></Chemical><Chemical><RegistryNumber>GAN16C9B8O</RegistryNumber><NameOfSubstance UI="D005978">Glutathione</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020134" MajorTopicYN="N">Catalytic Domain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000458" MajorTopicYN="N">Cyanobacteria</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015870" MajorTopicYN="N">Gene Expression</DescriptorName><QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D054477" MajorTopicYN="N">Glutaredoxins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005978" MajorTopicYN="N">Glutathione</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008027" MajorTopicYN="N">Light</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D062105" MajorTopicYN="N">Molecular Docking Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017433" MajorTopicYN="N">Protein Structure, Secondary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Cyanobacteria</Keyword><Keyword MajorTopicYN="N">Gene expression</Keyword><Keyword MajorTopicYN="N">Glutaredoxins</Keyword><Keyword MajorTopicYN="N">Glutathione</Keyword><Keyword MajorTopicYN="N">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="N">Protein modelling</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest Authors declare none conflicts of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>05</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>09</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>10</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31839562</ArticleId><ArticleId IdType="pii">S1476-9271(19)30419-0</ArticleId><ArticleId IdType="doi">10.1016/j.compbiolchem.2019.107141</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Mondal, Soumila" sort="Mondal, Soumila" uniqKey="Mondal S" first="Soumila" last="Mondal">Soumila Mondal</name></noRegion><name sortKey="Kumar, Vinod" sort="Kumar, Vinod" uniqKey="Kumar V" first="Vinod" last="Kumar">Vinod Kumar</name><name sortKey="Singh, Shailendra P" sort="Singh, Shailendra P" uniqKey="Singh S" first="Shailendra P" last="Singh">Shailendra P. 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