Reconstructing the evolutionary history of F420-dependent dehydrogenases View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

M. Laura Mascotti, Hemant Kumar, Quoc-Thai Nguyen, Maximiliano Juri Ayub, Marco W. Fraaije

ABSTRACT

During the last decade the number of characterized F420-dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F420-dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F420-dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F420-dependent dehydrogenases and the F420-dependent reductases. By such event, the dehydrogenases specialized in generating the reduced deazaflavin cofactor, while the reductases employ the reduced F420 for catalysis. Particularly, we focused on investigating the dehydrogenase subfamily and demonstrated that this group diversified into three types of dehydrogenases: the already known F420-dependent glucose-6-phosphate dehydrogenases, the F420-dependent alcohol dehydrogenases, and the sugar-6-phosphate dehydrogenases that were identified in this study. By reconstructing and experimentally characterizing ancestral and extant representatives of F420-dependent dehydrogenases, their biochemical properties were investigated and compared. We propose an evolutionary path for the emergence and diversification of the TIM-barrel fold F420-dependent dehydrogenases subfamily. More... »

PAGES

17571

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-018-35590-2

DOI

http://dx.doi.org/10.1038/s41598-018-35590-2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1110288643

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30514849


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "National University of San Luis", 
          "id": "https://www.grid.ac/institutes/grid.412115.2", 
          "name": [
            "IMIBIO-SL CONICET, Facultad de Qu\u00edmica Bioqu\u00edmica y Farmacia, Universidad Nacional de San Luis, Ej\u00e9rcito de los Andes 950, D5700HHW, San Luis, Argentina"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mascotti", 
        "givenName": "M. Laura", 
        "id": "sg:person.0756564426.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756564426.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Groningen", 
          "id": "https://www.grid.ac/institutes/grid.4830.f", 
          "name": [
            "Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kumar", 
        "givenName": "Hemant", 
        "id": "sg:person.011147155023.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011147155023.29"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ho Chi Minh City Medicine and Pharmacy University", 
          "id": "https://www.grid.ac/institutes/grid.413054.7", 
          "name": [
            "Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands", 
            "Scuola Universitaria Superiore IUSS Pavia, Piazza della Vittoria 15, 27100, Pavia, Italy", 
            "Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, 41 Dinh Tien Hoang Street, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nguyen", 
        "givenName": "Quoc-Thai", 
        "id": "sg:person.0606467563.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0606467563.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National University of San Luis", 
          "id": "https://www.grid.ac/institutes/grid.412115.2", 
          "name": [
            "IMIBIO-SL CONICET, Facultad de Qu\u00edmica Bioqu\u00edmica y Farmacia, Universidad Nacional de San Luis, Ej\u00e9rcito de los Andes 950, D5700HHW, San Luis, Argentina"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ayub", 
        "givenName": "Maximiliano Juri", 
        "id": "sg:person.01303334543.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01303334543.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Groningen", 
          "id": "https://www.grid.ac/institutes/grid.4830.f", 
          "name": [
            "Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fraaije", 
        "givenName": "Marco W.", 
        "id": "sg:person.0652316424.03", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0652316424.03"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1128/jb.00255-08", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002169514"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00253-016-8038-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005618081", 
          "https://doi.org/10.1007/s00253-016-8038-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00253-016-8038-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005618081", 
          "https://doi.org/10.1007/s00253-016-8038-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ismej.2016.100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005987834", 
          "https://doi.org/10.1038/ismej.2016.100"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1003653107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006446325"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1003653107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006446325"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1742-4658.2007.05740.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008877838"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkr367", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012248325"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0045003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014180527"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.95.12.6854", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014187443"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0081985", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014838380"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.str.2011.11.001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015471589"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/protein/11.10.855", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015934605"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/c2cy20129a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017335739"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.87.12.4576", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018027137"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s1399004715017939", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019179333"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m109.074310", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020916993"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkv1344", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022063719"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/prot.22964", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026541306"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gku947", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027840351"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2015.09.021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029226526"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btm477", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031802456"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1432-1033.1991.tb21046.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032885618"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1110/ps.041289805", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033518350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1110/ps.041289805", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033518350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(02)01069-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033844798"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(02)01069-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033844798"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2016.07.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034294491"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0959-440x(02)00284-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035069954"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2010.07356.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036873519"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2010.07356.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036873519"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkw408", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039393114"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0132689", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039854772"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msv037", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041179071"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/mmi.13378", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042051230"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg2689", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045071161", 
          "https://doi.org/10.1038/nrg2689"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg2689", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045071161", 
          "https://doi.org/10.1038/nrg2689"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkw1107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045738607"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m801854200", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045913510"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.00425-10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048958397"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(03)00949-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049185614"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(03)00949-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049185614"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.str.2004.02.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049756370"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/acs.biochem.6b00638", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055081690"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ar00127a004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055149144"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi00300a028", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055169268"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi00615a002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055182754"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi900003t", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055209473"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi900003t", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055209473"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msw223", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059923328"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aah3717", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062668387"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.02500-16", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062710426"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.01035-15", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062711740"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mmbr.00070-15", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062713823"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.178.10.2861-2866.1996", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062724816"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.toxicon.2017.06.012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1086144998"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2018-12", 
    "datePublishedReg": "2018-12-01", 
    "description": "During the last decade the number of characterized F420-dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F420-dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F420-dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F420-dependent dehydrogenases and the F420-dependent reductases. By such event, the dehydrogenases specialized in generating the reduced deazaflavin cofactor, while the reductases employ the reduced F420 for catalysis. Particularly, we focused on investigating the dehydrogenase subfamily and demonstrated that this group diversified into three types of dehydrogenases: the already known F420-dependent glucose-6-phosphate dehydrogenases, the F420-dependent alcohol dehydrogenases, and the sugar-6-phosphate dehydrogenases that were identified in this study. By reconstructing and experimentally characterizing ancestral and extant representatives of F420-dependent dehydrogenases, their biochemical properties were investigated and compared. We propose an evolutionary path for the emergence and diversification of the TIM-barrel fold F420-dependent dehydrogenases subfamily.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/s41598-018-35590-2", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1045337", 
        "issn": [
          "2045-2322"
        ], 
        "name": "Scientific Reports", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "8"
      }
    ], 
    "name": "Reconstructing the evolutionary history of F420-dependent dehydrogenases", 
    "pagination": "17571", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "ea6436ca1818487ff5be2920ee5d9692af99fccd848c6df11f05bca7fab9e506"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30514849"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101563288"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41598-018-35590-2"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1110288643"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41598-018-35590-2", 
      "https://app.dimensions.ai/details/publication/pub.1110288643"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T08:20", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000289_0000000289/records_95837_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/s41598-018-35590-2"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-35590-2'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-35590-2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-35590-2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-35590-2'


 

This table displays all metadata directly associated to this object as RDF triples.

251 TRIPLES      21 PREDICATES      77 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41598-018-35590-2 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N68d6a80145ca40c6823c491b0c9f0eaa
4 schema:citation sg:pub.10.1007/s00253-016-8038-y
5 sg:pub.10.1038/ismej.2016.100
6 sg:pub.10.1038/nrg2689
7 https://doi.org/10.1002/prot.22964
8 https://doi.org/10.1016/j.jmb.2015.09.021
9 https://doi.org/10.1016/j.jmb.2016.07.003
10 https://doi.org/10.1016/j.str.2004.02.010
11 https://doi.org/10.1016/j.str.2011.11.001
12 https://doi.org/10.1016/j.toxicon.2017.06.012
13 https://doi.org/10.1016/s0022-2836(02)01069-0
14 https://doi.org/10.1016/s0022-2836(03)00949-5
15 https://doi.org/10.1016/s0959-440x(02)00284-1
16 https://doi.org/10.1021/acs.biochem.6b00638
17 https://doi.org/10.1021/ar00127a004
18 https://doi.org/10.1021/bi00300a028
19 https://doi.org/10.1021/bi00615a002
20 https://doi.org/10.1021/bi900003t
21 https://doi.org/10.1039/c2cy20129a
22 https://doi.org/10.1073/pnas.1003653107
23 https://doi.org/10.1073/pnas.87.12.4576
24 https://doi.org/10.1073/pnas.95.12.6854
25 https://doi.org/10.1074/jbc.m109.074310
26 https://doi.org/10.1074/jbc.m801854200
27 https://doi.org/10.1093/bioinformatics/btm477
28 https://doi.org/10.1093/molbev/msv037
29 https://doi.org/10.1093/molbev/msw223
30 https://doi.org/10.1093/nar/gkr367
31 https://doi.org/10.1093/nar/gku947
32 https://doi.org/10.1093/nar/gkv1344
33 https://doi.org/10.1093/nar/gkw1107
34 https://doi.org/10.1093/nar/gkw408
35 https://doi.org/10.1093/protein/11.10.855
36 https://doi.org/10.1107/s1399004715017939
37 https://doi.org/10.1110/ps.041289805
38 https://doi.org/10.1111/j.1365-2958.2010.07356.x
39 https://doi.org/10.1111/j.1432-1033.1991.tb21046.x
40 https://doi.org/10.1111/j.1742-4658.2007.05740.x
41 https://doi.org/10.1111/mmi.13378
42 https://doi.org/10.1126/science.aah3717
43 https://doi.org/10.1128/aem.02500-16
44 https://doi.org/10.1128/jb.00255-08
45 https://doi.org/10.1128/jb.00425-10
46 https://doi.org/10.1128/jb.01035-15
47 https://doi.org/10.1128/jb.178.10.2861-2866.1996
48 https://doi.org/10.1128/mmbr.00070-15
49 https://doi.org/10.1371/journal.pone.0045003
50 https://doi.org/10.1371/journal.pone.0081985
51 https://doi.org/10.1371/journal.pone.0132689
52 schema:datePublished 2018-12
53 schema:datePublishedReg 2018-12-01
54 schema:description During the last decade the number of characterized F<sub>420</sub>-dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F<sub>420</sub>-dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F<sub>420</sub>-dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F<sub>420</sub>-dependent dehydrogenases and the F<sub>420</sub>-dependent reductases. By such event, the dehydrogenases specialized in generating the reduced deazaflavin cofactor, while the reductases employ the reduced F<sub>420</sub> for catalysis. Particularly, we focused on investigating the dehydrogenase subfamily and demonstrated that this group diversified into three types of dehydrogenases: the already known F<sub>420</sub>-dependent glucose-6-phosphate dehydrogenases, the F<sub>420</sub>-dependent alcohol dehydrogenases, and the sugar-6-phosphate dehydrogenases that were identified in this study. By reconstructing and experimentally characterizing ancestral and extant representatives of F<sub>420</sub>-dependent dehydrogenases, their biochemical properties were investigated and compared. We propose an evolutionary path for the emergence and diversification of the TIM-barrel fold F<sub>420</sub>-dependent dehydrogenases subfamily.
55 schema:genre research_article
56 schema:inLanguage en
57 schema:isAccessibleForFree true
58 schema:isPartOf Nbcbd4b3b303a4819ab9c376f43a6ec6a
59 Nd9e20a57b9904fb6b04797194c15496d
60 sg:journal.1045337
61 schema:name Reconstructing the evolutionary history of F420-dependent dehydrogenases
62 schema:pagination 17571
63 schema:productId N16e7f3813aee4414abf28bf6430e546f
64 N4dc49b518307475889839ed26328eb57
65 N57ecb0a27f6c496297738211374db174
66 N9c5ae46a9473452e93412a911c1fb864
67 Ne7fe3251473946419a4db9d078a60b7a
68 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110288643
69 https://doi.org/10.1038/s41598-018-35590-2
70 schema:sdDatePublished 2019-04-11T08:20
71 schema:sdLicense https://scigraph.springernature.com/explorer/license/
72 schema:sdPublisher N74da6863112f4b7883353f8eeb69ca1b
73 schema:url https://www.nature.com/articles/s41598-018-35590-2
74 sgo:license sg:explorer/license/
75 sgo:sdDataset articles
76 rdf:type schema:ScholarlyArticle
77 N16e7f3813aee4414abf28bf6430e546f schema:name dimensions_id
78 schema:value pub.1110288643
79 rdf:type schema:PropertyValue
80 N317e27912c384e7789d151a1e7335529 rdf:first sg:person.011147155023.29
81 rdf:rest Ne0b7998cc39f4759861d89543873d883
82 N3e4d92ee5fae40f98151acdfc10c4227 rdf:first sg:person.01303334543.02
83 rdf:rest N772f043cf934427cb19b185bf93f0263
84 N4dc49b518307475889839ed26328eb57 schema:name doi
85 schema:value 10.1038/s41598-018-35590-2
86 rdf:type schema:PropertyValue
87 N57ecb0a27f6c496297738211374db174 schema:name readcube_id
88 schema:value ea6436ca1818487ff5be2920ee5d9692af99fccd848c6df11f05bca7fab9e506
89 rdf:type schema:PropertyValue
90 N68d6a80145ca40c6823c491b0c9f0eaa rdf:first sg:person.0756564426.25
91 rdf:rest N317e27912c384e7789d151a1e7335529
92 N74da6863112f4b7883353f8eeb69ca1b schema:name Springer Nature - SN SciGraph project
93 rdf:type schema:Organization
94 N772f043cf934427cb19b185bf93f0263 rdf:first sg:person.0652316424.03
95 rdf:rest rdf:nil
96 N9c5ae46a9473452e93412a911c1fb864 schema:name pubmed_id
97 schema:value 30514849
98 rdf:type schema:PropertyValue
99 Nbcbd4b3b303a4819ab9c376f43a6ec6a schema:issueNumber 1
100 rdf:type schema:PublicationIssue
101 Nd9e20a57b9904fb6b04797194c15496d schema:volumeNumber 8
102 rdf:type schema:PublicationVolume
103 Ne0b7998cc39f4759861d89543873d883 rdf:first sg:person.0606467563.13
104 rdf:rest N3e4d92ee5fae40f98151acdfc10c4227
105 Ne7fe3251473946419a4db9d078a60b7a schema:name nlm_unique_id
106 schema:value 101563288
107 rdf:type schema:PropertyValue
108 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
109 schema:name Biological Sciences
110 rdf:type schema:DefinedTerm
111 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
112 schema:name Genetics
113 rdf:type schema:DefinedTerm
114 sg:journal.1045337 schema:issn 2045-2322
115 schema:name Scientific Reports
116 rdf:type schema:Periodical
117 sg:person.011147155023.29 schema:affiliation https://www.grid.ac/institutes/grid.4830.f
118 schema:familyName Kumar
119 schema:givenName Hemant
120 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011147155023.29
121 rdf:type schema:Person
122 sg:person.01303334543.02 schema:affiliation https://www.grid.ac/institutes/grid.412115.2
123 schema:familyName Ayub
124 schema:givenName Maximiliano Juri
125 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01303334543.02
126 rdf:type schema:Person
127 sg:person.0606467563.13 schema:affiliation https://www.grid.ac/institutes/grid.413054.7
128 schema:familyName Nguyen
129 schema:givenName Quoc-Thai
130 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0606467563.13
131 rdf:type schema:Person
132 sg:person.0652316424.03 schema:affiliation https://www.grid.ac/institutes/grid.4830.f
133 schema:familyName Fraaije
134 schema:givenName Marco W.
135 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0652316424.03
136 rdf:type schema:Person
137 sg:person.0756564426.25 schema:affiliation https://www.grid.ac/institutes/grid.412115.2
138 schema:familyName Mascotti
139 schema:givenName M. Laura
140 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756564426.25
141 rdf:type schema:Person
142 sg:pub.10.1007/s00253-016-8038-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1005618081
143 https://doi.org/10.1007/s00253-016-8038-y
144 rdf:type schema:CreativeWork
145 sg:pub.10.1038/ismej.2016.100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005987834
146 https://doi.org/10.1038/ismej.2016.100
147 rdf:type schema:CreativeWork
148 sg:pub.10.1038/nrg2689 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045071161
149 https://doi.org/10.1038/nrg2689
150 rdf:type schema:CreativeWork
151 https://doi.org/10.1002/prot.22964 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026541306
152 rdf:type schema:CreativeWork
153 https://doi.org/10.1016/j.jmb.2015.09.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029226526
154 rdf:type schema:CreativeWork
155 https://doi.org/10.1016/j.jmb.2016.07.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034294491
156 rdf:type schema:CreativeWork
157 https://doi.org/10.1016/j.str.2004.02.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049756370
158 rdf:type schema:CreativeWork
159 https://doi.org/10.1016/j.str.2011.11.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015471589
160 rdf:type schema:CreativeWork
161 https://doi.org/10.1016/j.toxicon.2017.06.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1086144998
162 rdf:type schema:CreativeWork
163 https://doi.org/10.1016/s0022-2836(02)01069-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033844798
164 rdf:type schema:CreativeWork
165 https://doi.org/10.1016/s0022-2836(03)00949-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049185614
166 rdf:type schema:CreativeWork
167 https://doi.org/10.1016/s0959-440x(02)00284-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035069954
168 rdf:type schema:CreativeWork
169 https://doi.org/10.1021/acs.biochem.6b00638 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055081690
170 rdf:type schema:CreativeWork
171 https://doi.org/10.1021/ar00127a004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055149144
172 rdf:type schema:CreativeWork
173 https://doi.org/10.1021/bi00300a028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055169268
174 rdf:type schema:CreativeWork
175 https://doi.org/10.1021/bi00615a002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055182754
176 rdf:type schema:CreativeWork
177 https://doi.org/10.1021/bi900003t schema:sameAs https://app.dimensions.ai/details/publication/pub.1055209473
178 rdf:type schema:CreativeWork
179 https://doi.org/10.1039/c2cy20129a schema:sameAs https://app.dimensions.ai/details/publication/pub.1017335739
180 rdf:type schema:CreativeWork
181 https://doi.org/10.1073/pnas.1003653107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006446325
182 rdf:type schema:CreativeWork
183 https://doi.org/10.1073/pnas.87.12.4576 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018027137
184 rdf:type schema:CreativeWork
185 https://doi.org/10.1073/pnas.95.12.6854 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014187443
186 rdf:type schema:CreativeWork
187 https://doi.org/10.1074/jbc.m109.074310 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020916993
188 rdf:type schema:CreativeWork
189 https://doi.org/10.1074/jbc.m801854200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045913510
190 rdf:type schema:CreativeWork
191 https://doi.org/10.1093/bioinformatics/btm477 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031802456
192 rdf:type schema:CreativeWork
193 https://doi.org/10.1093/molbev/msv037 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041179071
194 rdf:type schema:CreativeWork
195 https://doi.org/10.1093/molbev/msw223 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059923328
196 rdf:type schema:CreativeWork
197 https://doi.org/10.1093/nar/gkr367 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012248325
198 rdf:type schema:CreativeWork
199 https://doi.org/10.1093/nar/gku947 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027840351
200 rdf:type schema:CreativeWork
201 https://doi.org/10.1093/nar/gkv1344 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022063719
202 rdf:type schema:CreativeWork
203 https://doi.org/10.1093/nar/gkw1107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045738607
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1093/nar/gkw408 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039393114
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1093/protein/11.10.855 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015934605
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1107/s1399004715017939 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019179333
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1110/ps.041289805 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033518350
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1111/j.1365-2958.2010.07356.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1036873519
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1111/j.1432-1033.1991.tb21046.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1032885618
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1111/j.1742-4658.2007.05740.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1008877838
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1111/mmi.13378 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042051230
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1126/science.aah3717 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062668387
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1128/aem.02500-16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062710426
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1128/jb.00255-08 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002169514
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1128/jb.00425-10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048958397
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1128/jb.01035-15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062711740
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1128/jb.178.10.2861-2866.1996 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062724816
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1128/mmbr.00070-15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062713823
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1371/journal.pone.0045003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014180527
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1371/journal.pone.0081985 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014838380
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1371/journal.pone.0132689 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039854772
240 rdf:type schema:CreativeWork
241 https://www.grid.ac/institutes/grid.412115.2 schema:alternateName National University of San Luis
242 schema:name IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW, San Luis, Argentina
243 rdf:type schema:Organization
244 https://www.grid.ac/institutes/grid.413054.7 schema:alternateName Ho Chi Minh City Medicine and Pharmacy University
245 schema:name Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, 41 Dinh Tien Hoang Street, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
246 Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
247 Scuola Universitaria Superiore IUSS Pavia, Piazza della Vittoria 15, 27100, Pavia, Italy
248 rdf:type schema:Organization
249 https://www.grid.ac/institutes/grid.4830.f schema:alternateName University of Groningen
250 schema:name Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
251 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...