Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-02

AUTHORS

Kayo Nozawa, Patrick O’Donoghue, Sarath Gundllapalli, Yuhei Araiso, Ryuichiro Ishitani, Takuya Umehara, Dieter Söll, Osamu Nureki

ABSTRACT

Pyrrolysine (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality. More... »

PAGES

1163

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature07611

DOI

http://dx.doi.org/10.1038/nature07611

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1050344096

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19118381


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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Amino Acyl-tRNA Synthetases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Aminoacylation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Crystallography, X-Ray", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Desulfitobacterium", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Escherichia coli", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Lysine", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Methanosarcina barkeri", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Transfer, Amino Acid-Specific", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Structural Homology, Protein", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Tokyo Institute of Technology", 
          "id": "https://www.grid.ac/institutes/grid.32197.3e", 
          "name": [
            "Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nozawa", 
        "givenName": "Kayo", 
        "id": "sg:person.0704417421.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0704417421.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Molecular Biophysics and Biochemistry,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "O\u2019Donoghue", 
        "givenName": "Patrick", 
        "id": "sg:person.0710542277.93", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0710542277.93"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Molecular Biophysics and Biochemistry,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gundllapalli", 
        "givenName": "Sarath", 
        "id": "sg:person.012767421337.44", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012767421337.44"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Tokyo Institute of Technology", 
          "id": "https://www.grid.ac/institutes/grid.32197.3e", 
          "name": [
            "Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Araiso", 
        "givenName": "Yuhei", 
        "id": "sg:person.01251604577.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01251604577.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ishitani", 
        "givenName": "Ryuichiro", 
        "id": "sg:person.01221724404.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01221724404.09"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Molecular Biophysics and Biochemistry,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Umehara", 
        "givenName": "Takuya", 
        "id": "sg:person.01217257316.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01217257316.69"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Yale University", 
          "id": "https://www.grid.ac/institutes/grid.47100.32", 
          "name": [
            "Department of Molecular Biophysics and Biochemistry,", 
            "Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "S\u00f6ll", 
        "givenName": "Dieter", 
        "id": "sg:person.012067245622.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012067245622.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan", 
            "Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nureki", 
        "givenName": "Osamu", 
        "id": "sg:person.01043223704.15", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043223704.15"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/j.febslet.2007.06.004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005289941"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0263-7855(96)00018-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005898005"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mib.2005.10.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006260023"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mib.2005.10.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006260023"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-382", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010632421", 
          "https://doi.org/10.1186/1471-2105-7-382"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-382", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010632421", 
          "https://doi.org/10.1186/1471-2105-7-382"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm869", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011248126"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm514", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011527288"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(00)80746-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012412174"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbrc.2008.07.074", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014022345"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0108767390010224", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014210169"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.febslet.2006.11.028", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015806699"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.ge.19.120185.000421", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015963628"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0611634104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017430856"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nchembio.73", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018517323", 
          "https://doi.org/10.1038/nchembio.73"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0704769104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019469535"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0021889897006766", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019562892"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444998003254", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019779527"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mmbr.67.4.550-573.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020797287"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl1151", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021571457"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1134/s0006297907030029", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024844800", 
          "https://doi.org/10.1134/s0006297907030029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1134/s0006297907030029", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024844800", 
          "https://doi.org/10.1134/s0006297907030029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02895", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032544082", 
          "https://doi.org/10.1038/nature02895"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02895", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032544082", 
          "https://doi.org/10.1038/nature02895"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1069588", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033064323"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh266", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033530521"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2008.02.045", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034884603"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/28.1.235", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035055456"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0969-2126(97)00166-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039889419"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/18.22.6532", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041216985"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.biophys.35.101105.121507", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041935877"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jmbi.2000.3819", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046204497"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0405362101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047104503"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1017/s1355838202022021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1054923762"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi060491l", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055201920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi060491l", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055201920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.2047877", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062519697"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.8128220", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062652859"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1080438866", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/j.1460-2075.1994.tb06265.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1082752620"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2009-02", 
    "datePublishedReg": "2009-02-01", 
    "description": "Pyrrolysine (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nature07611", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2508989", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7233", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "457"
      }
    ], 
    "name": "Pyrrolysyl-tRNA synthetase\u2013tRNAPyl structure reveals the molecular basis of orthogonality", 
    "pagination": "1163", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "efd326c2aba2e0f3a1d46e6467a6d776a8a33aa95fc34e2e479d3db2d5ffb5c8"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19118381"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nature07611"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1050344096"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nature07611", 
      "https://app.dimensions.ai/details/publication/pub.1050344096"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T12:59", 
    "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/v90/0000000001_0000000264/records_8659_00000426.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nature07611"
  }
]
 

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/nature07611'

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/nature07611'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature07611'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature07611'


 

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

282 TRIPLES      21 PREDICATES      74 URIs      31 LITERALS      19 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nature07611 schema:about N1e77a8d6633b43628cb404e8857dde9c
2 N4fb1561f999d4d4dab635b1bc2e536b2
3 N705afe18948e4b4bbf3d1b7a70a7fd25
4 Na15840ccd3364894bb6382f556a3eb19
5 Nc50c3a0124ba4ba183250b334de78155
6 Nc7e04082e5d7402c98e70294c1f1e721
7 Nd21d1f2a236d44439a739884d83152c8
8 Nd9f8222ddb954d898e2ec1f734e9044b
9 Nf2ca85228f754101bc86f67feba889b0
10 Nf8f5b4a2ff494b0080260f19092809ff
11 anzsrc-for:06
12 anzsrc-for:0604
13 schema:author N76b883a6cf5844d2986897180046ed3d
14 schema:citation sg:pub.10.1038/nature02895
15 sg:pub.10.1038/nchembio.73
16 sg:pub.10.1134/s0006297907030029
17 sg:pub.10.1186/1471-2105-7-382
18 https://app.dimensions.ai/details/publication/pub.1080438866
19 https://doi.org/10.1002/j.1460-2075.1994.tb06265.x
20 https://doi.org/10.1006/jmbi.2000.3819
21 https://doi.org/10.1016/0263-7855(96)00018-5
22 https://doi.org/10.1016/j.bbrc.2008.07.074
23 https://doi.org/10.1016/j.febslet.2006.11.028
24 https://doi.org/10.1016/j.febslet.2007.06.004
25 https://doi.org/10.1016/j.jmb.2008.02.045
26 https://doi.org/10.1016/j.mib.2005.10.009
27 https://doi.org/10.1016/s0092-8674(00)80746-1
28 https://doi.org/10.1016/s0969-2126(97)00166-4
29 https://doi.org/10.1017/s1355838202022021
30 https://doi.org/10.1021/bi060491l
31 https://doi.org/10.1073/pnas.0405362101
32 https://doi.org/10.1073/pnas.0611634104
33 https://doi.org/10.1073/pnas.0704769104
34 https://doi.org/10.1093/emboj/18.22.6532
35 https://doi.org/10.1093/nar/28.1.235
36 https://doi.org/10.1093/nar/gkh266
37 https://doi.org/10.1093/nar/gkl1151
38 https://doi.org/10.1093/nar/gkm514
39 https://doi.org/10.1093/nar/gkm869
40 https://doi.org/10.1107/s0021889897006766
41 https://doi.org/10.1107/s0108767390010224
42 https://doi.org/10.1107/s0907444998003254
43 https://doi.org/10.1126/science.1069588
44 https://doi.org/10.1126/science.2047877
45 https://doi.org/10.1126/science.8128220
46 https://doi.org/10.1128/mmbr.67.4.550-573.2003
47 https://doi.org/10.1146/annurev.biophys.35.101105.121507
48 https://doi.org/10.1146/annurev.ge.19.120185.000421
49 schema:datePublished 2009-02
50 schema:datePublishedReg 2009-02-01
51 schema:description Pyrrolysine (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality.
52 schema:genre research_article
53 schema:inLanguage en
54 schema:isAccessibleForFree true
55 schema:isPartOf Nbffe6bdb261d49ffb1db11f643384853
56 Ne83a4dd59ecd45bcaae5a785a4825558
57 sg:journal.1018957
58 schema:name Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality
59 schema:pagination 1163
60 schema:productId N02669d871afa45ed9ac93b94583d17b5
61 Nbd84fd899b694fce81a174973599ca09
62 Nc58eb336cd6d449ab0d7dbd156a5c19e
63 Nc8d65b3485634774a4b94d626ce829fe
64 Ne6449cef1e3b430abfcfc72f07bed98b
65 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050344096
66 https://doi.org/10.1038/nature07611
67 schema:sdDatePublished 2019-04-10T12:59
68 schema:sdLicense https://scigraph.springernature.com/explorer/license/
69 schema:sdPublisher N4e49668c4fe64b21b50766bac1730c70
70 schema:url https://www.nature.com/articles/nature07611
71 sgo:license sg:explorer/license/
72 sgo:sdDataset articles
73 rdf:type schema:ScholarlyArticle
74 N02669d871afa45ed9ac93b94583d17b5 schema:name pubmed_id
75 schema:value 19118381
76 rdf:type schema:PropertyValue
77 N1e77a8d6633b43628cb404e8857dde9c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Structural Homology, Protein
79 rdf:type schema:DefinedTerm
80 N21ff1bd474564112a9a3e816899c78fb rdf:first sg:person.0710542277.93
81 rdf:rest N5b67bf03448f4a258d2dbfe83aaa1ce4
82 N2a67580ccdb949e494ee97cabfd39ebe rdf:first sg:person.01217257316.69
83 rdf:rest N450146e56b6f4b62960e213db455b6ca
84 N38e1b7ed2d464d5384a3ec050ae3d0a0 schema:name Department of Molecular Biophysics and Biochemistry,
85 rdf:type schema:Organization
86 N450146e56b6f4b62960e213db455b6ca rdf:first sg:person.012067245622.45
87 rdf:rest Ne2543b3a132b4178ab82a79ba3023789
88 N4e49668c4fe64b21b50766bac1730c70 schema:name Springer Nature - SN SciGraph project
89 rdf:type schema:Organization
90 N4fb1561f999d4d4dab635b1bc2e536b2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Lysine
92 rdf:type schema:DefinedTerm
93 N569147d73571437694ba60c1b4b9c689 rdf:first sg:person.01251604577.19
94 rdf:rest Nec41749e175c4ee1bfb1969553590968
95 N5b67bf03448f4a258d2dbfe83aaa1ce4 rdf:first sg:person.012767421337.44
96 rdf:rest N569147d73571437694ba60c1b4b9c689
97 N705afe18948e4b4bbf3d1b7a70a7fd25 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Crystallography, X-Ray
99 rdf:type schema:DefinedTerm
100 N76b883a6cf5844d2986897180046ed3d rdf:first sg:person.0704417421.10
101 rdf:rest N21ff1bd474564112a9a3e816899c78fb
102 Na13ea9255a794f89b8124a1c19c44bd6 schema:name Department of Molecular Biophysics and Biochemistry,
103 rdf:type schema:Organization
104 Na15840ccd3364894bb6382f556a3eb19 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Desulfitobacterium
106 rdf:type schema:DefinedTerm
107 Nb64fb7103bca46f685a4242a40754134 schema:name Department of Molecular Biophysics and Biochemistry,
108 rdf:type schema:Organization
109 Nbd84fd899b694fce81a174973599ca09 schema:name readcube_id
110 schema:value efd326c2aba2e0f3a1d46e6467a6d776a8a33aa95fc34e2e479d3db2d5ffb5c8
111 rdf:type schema:PropertyValue
112 Nbffe6bdb261d49ffb1db11f643384853 schema:issueNumber 7233
113 rdf:type schema:PublicationIssue
114 Nc50c3a0124ba4ba183250b334de78155 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Methanosarcina barkeri
116 rdf:type schema:DefinedTerm
117 Nc58eb336cd6d449ab0d7dbd156a5c19e schema:name doi
118 schema:value 10.1038/nature07611
119 rdf:type schema:PropertyValue
120 Nc7e04082e5d7402c98e70294c1f1e721 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
121 schema:name Amino Acyl-tRNA Synthetases
122 rdf:type schema:DefinedTerm
123 Nc8d65b3485634774a4b94d626ce829fe schema:name nlm_unique_id
124 schema:value 0410462
125 rdf:type schema:PropertyValue
126 Nd21d1f2a236d44439a739884d83152c8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Models, Molecular
128 rdf:type schema:DefinedTerm
129 Nd9f8222ddb954d898e2ec1f734e9044b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
130 schema:name Aminoacylation
131 rdf:type schema:DefinedTerm
132 Ne2543b3a132b4178ab82a79ba3023789 rdf:first sg:person.01043223704.15
133 rdf:rest rdf:nil
134 Ne6449cef1e3b430abfcfc72f07bed98b schema:name dimensions_id
135 schema:value pub.1050344096
136 rdf:type schema:PropertyValue
137 Ne83a4dd59ecd45bcaae5a785a4825558 schema:volumeNumber 457
138 rdf:type schema:PublicationVolume
139 Nec41749e175c4ee1bfb1969553590968 rdf:first sg:person.01221724404.09
140 rdf:rest N2a67580ccdb949e494ee97cabfd39ebe
141 Nf2ca85228f754101bc86f67feba889b0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
142 schema:name RNA, Transfer, Amino Acid-Specific
143 rdf:type schema:DefinedTerm
144 Nf8f5b4a2ff494b0080260f19092809ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
145 schema:name Escherichia coli
146 rdf:type schema:DefinedTerm
147 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
148 schema:name Biological Sciences
149 rdf:type schema:DefinedTerm
150 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
151 schema:name Genetics
152 rdf:type schema:DefinedTerm
153 sg:grant.2508989 http://pending.schema.org/fundedItem sg:pub.10.1038/nature07611
154 rdf:type schema:MonetaryGrant
155 sg:journal.1018957 schema:issn 0090-0028
156 1476-4687
157 schema:name Nature
158 rdf:type schema:Periodical
159 sg:person.01043223704.15 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
160 schema:familyName Nureki
161 schema:givenName Osamu
162 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043223704.15
163 rdf:type schema:Person
164 sg:person.012067245622.45 schema:affiliation https://www.grid.ac/institutes/grid.47100.32
165 schema:familyName Söll
166 schema:givenName Dieter
167 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012067245622.45
168 rdf:type schema:Person
169 sg:person.01217257316.69 schema:affiliation N38e1b7ed2d464d5384a3ec050ae3d0a0
170 schema:familyName Umehara
171 schema:givenName Takuya
172 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01217257316.69
173 rdf:type schema:Person
174 sg:person.01221724404.09 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
175 schema:familyName Ishitani
176 schema:givenName Ryuichiro
177 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01221724404.09
178 rdf:type schema:Person
179 sg:person.01251604577.19 schema:affiliation https://www.grid.ac/institutes/grid.32197.3e
180 schema:familyName Araiso
181 schema:givenName Yuhei
182 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01251604577.19
183 rdf:type schema:Person
184 sg:person.012767421337.44 schema:affiliation Na13ea9255a794f89b8124a1c19c44bd6
185 schema:familyName Gundllapalli
186 schema:givenName Sarath
187 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012767421337.44
188 rdf:type schema:Person
189 sg:person.0704417421.10 schema:affiliation https://www.grid.ac/institutes/grid.32197.3e
190 schema:familyName Nozawa
191 schema:givenName Kayo
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0704417421.10
193 rdf:type schema:Person
194 sg:person.0710542277.93 schema:affiliation Nb64fb7103bca46f685a4242a40754134
195 schema:familyName O’Donoghue
196 schema:givenName Patrick
197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0710542277.93
198 rdf:type schema:Person
199 sg:pub.10.1038/nature02895 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032544082
200 https://doi.org/10.1038/nature02895
201 rdf:type schema:CreativeWork
202 sg:pub.10.1038/nchembio.73 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018517323
203 https://doi.org/10.1038/nchembio.73
204 rdf:type schema:CreativeWork
205 sg:pub.10.1134/s0006297907030029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024844800
206 https://doi.org/10.1134/s0006297907030029
207 rdf:type schema:CreativeWork
208 sg:pub.10.1186/1471-2105-7-382 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010632421
209 https://doi.org/10.1186/1471-2105-7-382
210 rdf:type schema:CreativeWork
211 https://app.dimensions.ai/details/publication/pub.1080438866 schema:CreativeWork
212 https://doi.org/10.1002/j.1460-2075.1994.tb06265.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1082752620
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1006/jmbi.2000.3819 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046204497
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1016/0263-7855(96)00018-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005898005
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1016/j.bbrc.2008.07.074 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014022345
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1016/j.febslet.2006.11.028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015806699
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1016/j.febslet.2007.06.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005289941
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1016/j.jmb.2008.02.045 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034884603
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1016/j.mib.2005.10.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006260023
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1016/s0092-8674(00)80746-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012412174
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1016/s0969-2126(97)00166-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039889419
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1017/s1355838202022021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054923762
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1021/bi060491l schema:sameAs https://app.dimensions.ai/details/publication/pub.1055201920
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1073/pnas.0405362101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047104503
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1073/pnas.0611634104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017430856
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1073/pnas.0704769104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019469535
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1093/emboj/18.22.6532 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041216985
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1093/nar/28.1.235 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035055456
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1093/nar/gkh266 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033530521
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1093/nar/gkl1151 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021571457
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1093/nar/gkm514 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011527288
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1093/nar/gkm869 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011248126
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1107/s0021889897006766 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019562892
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1107/s0108767390010224 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014210169
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1107/s0907444998003254 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019779527
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1126/science.1069588 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033064323
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1126/science.2047877 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062519697
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1126/science.8128220 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062652859
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1128/mmbr.67.4.550-573.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020797287
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1146/annurev.biophys.35.101105.121507 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041935877
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1146/annurev.ge.19.120185.000421 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015963628
271 rdf:type schema:CreativeWork
272 https://www.grid.ac/institutes/grid.26999.3d schema:alternateName University of Tokyo
273 schema:name Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
274 Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
275 rdf:type schema:Organization
276 https://www.grid.ac/institutes/grid.32197.3e schema:alternateName Tokyo Institute of Technology
277 schema:name Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
278 rdf:type schema:Organization
279 https://www.grid.ac/institutes/grid.47100.32 schema:alternateName Yale University
280 schema:name Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114, USA
281 Department of Molecular Biophysics and Biochemistry,
282 rdf:type schema:Organization
 




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


...