A new understanding of the decoding principle on the ribosome View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2012-03-21

AUTHORS

Natalia Demeshkina, Lasse Jenner, Eric Westhof, Marat Yusupov, Gulnara Yusupova

ABSTRACT

During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome. More... »

PAGES

256

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature10913

DOI

http://dx.doi.org/10.1038/nature10913

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1022866252

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22437501


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/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "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": "Anticodon", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Pairing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Codon", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Crystallography, X-Ray", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Biological", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleic Acid Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Biosynthesis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Messenger", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Ribosomal, 23S", 
        "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": "Ribosomes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Thermus thermophilus", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "D\u00e9partement de Biologie et de G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Universit\u00e9 de Strasbourg, Strasbourg 67000, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Demeshkina", 
        "givenName": "Natalia", 
        "id": "sg:person.01232312222.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232312222.62"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "D\u00e9partement de Biologie et de G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Universit\u00e9 de Strasbourg, Strasbourg 67000, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jenner", 
        "givenName": "Lasse", 
        "id": "sg:person.0576270133.74", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0576270133.74"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute for Molecular and Cellular Biology", 
          "id": "https://www.grid.ac/institutes/grid.465534.5", 
          "name": [
            "Architecture et R\u00e9activit\u00e9 de l\u2019ARN, Universit\u00e9 de Strasbourg, Institut de Biologie Mol\u00e9culaire et Cellulaire, CNRS, Strasbourg 67084, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Westhof", 
        "givenName": "Eric", 
        "id": "sg:person.01242346450.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242346450.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "D\u00e9partement de Biologie et de G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Universit\u00e9 de Strasbourg, Strasbourg 67000, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yusupov", 
        "givenName": "Marat", 
        "id": "sg:person.0773543020.27", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773543020.27"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "D\u00e9partement de Biologie et de G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Universit\u00e9 de Strasbourg, Strasbourg 67000, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yusupova", 
        "givenName": "Gulnara", 
        "id": "sg:person.01313146525.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01313146525.30"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1261/rna.2035410", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000810396"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1060612", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002395498"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1131127", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003901838"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2009.01.036", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006013070"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.1577", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007018540", 
          "https://doi.org/10.1038/nsmb.1577"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.1790", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008900126", 
          "https://doi.org/10.1038/nsmb.1790"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(90)90016-f", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017742608"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909052925", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020777046"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909052925", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020777046"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022046953", 
          "https://doi.org/10.1038/nsmb.2003"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2010.04.038", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022144736"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444911049833", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023977440"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.1880", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027212590", 
          "https://doi.org/10.1038/nsmb.1880"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.febslet.2004.11.048", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027764924"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.biochem.70.1.415", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029650829"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1111408", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029815934"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0300-9084(86)80023-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030456101"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/emboj.2009.26", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032259085"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/72364", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033232899", 
          "https://doi.org/10.1038/72364"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1012825108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036625209"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909021933", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038618493"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tibs.2005.10.006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040890497"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tibs.2005.10.006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040890497"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1194460", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040923975"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(05)80023-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041097615"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/emboj.2008.243", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048490262"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(02)01086-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049702328"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2005.12.018", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049853767"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0705988104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053587492"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1017/s1355838201002382", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1054923649"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1179700", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062460594"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1179700", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062460594"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.285.5434.1722", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062566569"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012-03-21", 
    "datePublishedReg": "2012-03-21", 
    "description": "During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4\u2009\u00c5 resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U\u00b7G and G\u00b7U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C\u00b7G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nature10913", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3786087", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7393", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "484"
      }
    ], 
    "name": "A new understanding of the decoding principle on the ribosome", 
    "pagination": "256", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "6cf05d5cca823287bac2af6e948c6480d0a28d207d02c9c3268cdb93fd9712cd"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22437501"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nature10913"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1022866252"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nature10913", 
      "https://app.dimensions.ai/details/publication/pub.1022866252"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T23:13", 
    "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_8693_00000434.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nature10913"
  }
]
 

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/nature10913'

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/nature10913'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature10913'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature10913'


 

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

266 TRIPLES      21 PREDICATES      74 URIs      36 LITERALS      25 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nature10913 schema:about N196114b4af584e9e87d48cdd424f238c
2 N1d7a8048c55449ffaf007e2c2d977276
3 N28bc6ce3e033428fbf2679f30cda365e
4 N2e207534b19c42089edf960f795cec54
5 N3fd1a03f9bab4095b3498baf5ede80cb
6 N508cdfac4d3c476997a433c63688a4cd
7 N65908958591d49d79c585531cad90c85
8 N802718abbfea4917b0a567eb27ada2fb
9 N8f6ef066b300455eba8141fe2d53ac99
10 N9730fced215a4ae5865796565cf95de5
11 N9ace2ee0ef88413da88c58b9b441f137
12 Naae17696af594d75acd9a0b8ca4ec50e
13 Nc212ca8a58e2481482037dcc13bd8ff9
14 Nc54fcfaba3d647b5be19794e71910422
15 Ndae76cf7229b4c94b91eaa76779278ef
16 Ne5da4268c08446749e8dece47363d8e1
17 anzsrc-for:06
18 anzsrc-for:0601
19 schema:author Nbff9f241871b41cca19d96647e2b2ff6
20 schema:citation sg:pub.10.1038/72364
21 sg:pub.10.1038/nsmb.1577
22 sg:pub.10.1038/nsmb.1790
23 sg:pub.10.1038/nsmb.1880
24 sg:pub.10.1038/nsmb.2003
25 https://doi.org/10.1016/0022-2836(90)90016-f
26 https://doi.org/10.1016/j.cell.2009.01.036
27 https://doi.org/10.1016/j.febslet.2004.11.048
28 https://doi.org/10.1016/j.jmb.2010.04.038
29 https://doi.org/10.1016/j.molcel.2005.12.018
30 https://doi.org/10.1016/j.tibs.2005.10.006
31 https://doi.org/10.1016/s0022-2836(05)80023-3
32 https://doi.org/10.1016/s0092-8674(02)01086-3
33 https://doi.org/10.1016/s0300-9084(86)80023-2
34 https://doi.org/10.1017/s1355838201002382
35 https://doi.org/10.1038/emboj.2008.243
36 https://doi.org/10.1038/emboj.2009.26
37 https://doi.org/10.1073/pnas.0705988104
38 https://doi.org/10.1073/pnas.1012825108
39 https://doi.org/10.1107/s0907444909021933
40 https://doi.org/10.1107/s0907444909052925
41 https://doi.org/10.1107/s0907444911049833
42 https://doi.org/10.1126/science.1060612
43 https://doi.org/10.1126/science.1111408
44 https://doi.org/10.1126/science.1131127
45 https://doi.org/10.1126/science.1179700
46 https://doi.org/10.1126/science.1194460
47 https://doi.org/10.1126/science.285.5434.1722
48 https://doi.org/10.1146/annurev.biochem.70.1.415
49 https://doi.org/10.1261/rna.2035410
50 schema:datePublished 2012-03-21
51 schema:datePublishedReg 2012-03-21
52 schema:description During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.
53 schema:genre research_article
54 schema:inLanguage en
55 schema:isAccessibleForFree false
56 schema:isPartOf Nc9a992f776664b98bbc25f0490dfd820
57 Ncc735fd81e73402a865419e5d66a1e0a
58 sg:journal.1018957
59 schema:name A new understanding of the decoding principle on the ribosome
60 schema:pagination 256
61 schema:productId N2d2f6a6ab4e54ce689b849daa4b9da10
62 N4889e1cd9aec49bb8a38d47e138c5c79
63 N6997605deeab47938ddab0b4b59747bc
64 N9eaefc9b3b9342299575da6ee489b94d
65 Ne885b52ff2ea4a0db82236d490f8b2ac
66 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022866252
67 https://doi.org/10.1038/nature10913
68 schema:sdDatePublished 2019-04-10T23:13
69 schema:sdLicense https://scigraph.springernature.com/explorer/license/
70 schema:sdPublisher N7c5be15f4dbf48ac9a7fca091a4d9483
71 schema:url https://www.nature.com/articles/nature10913
72 sgo:license sg:explorer/license/
73 sgo:sdDataset articles
74 rdf:type schema:ScholarlyArticle
75 N10eb8c9d043d4f97896cbc9851e75026 schema:name Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Université de Strasbourg, Strasbourg 67000, France
76 rdf:type schema:Organization
77 N196114b4af584e9e87d48cdd424f238c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Anticodon
79 rdf:type schema:DefinedTerm
80 N1d7a8048c55449ffaf007e2c2d977276 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Ribosomes
82 rdf:type schema:DefinedTerm
83 N26c7db4a929d4f1e88e8691322ac5179 schema:name Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Université de Strasbourg, Strasbourg 67000, France
84 rdf:type schema:Organization
85 N28bc6ce3e033428fbf2679f30cda365e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Codon
87 rdf:type schema:DefinedTerm
88 N2d2f6a6ab4e54ce689b849daa4b9da10 schema:name readcube_id
89 schema:value 6cf05d5cca823287bac2af6e948c6480d0a28d207d02c9c3268cdb93fd9712cd
90 rdf:type schema:PropertyValue
91 N2e207534b19c42089edf960f795cec54 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Base Sequence
93 rdf:type schema:DefinedTerm
94 N3fd1a03f9bab4095b3498baf5ede80cb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
95 schema:name RNA, Transfer, Amino Acid-Specific
96 rdf:type schema:DefinedTerm
97 N461366bef3d5474eb8dc3b6fc5659ace rdf:first sg:person.0773543020.27
98 rdf:rest N8c1ee74c49204076b8de389bb9e40cc9
99 N4889e1cd9aec49bb8a38d47e138c5c79 schema:name nlm_unique_id
100 schema:value 0410462
101 rdf:type schema:PropertyValue
102 N508cdfac4d3c476997a433c63688a4cd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
103 schema:name Base Pairing
104 rdf:type schema:DefinedTerm
105 N65908958591d49d79c585531cad90c85 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Thermus thermophilus
107 rdf:type schema:DefinedTerm
108 N6997605deeab47938ddab0b4b59747bc schema:name doi
109 schema:value 10.1038/nature10913
110 rdf:type schema:PropertyValue
111 N75f313d54814468ab4c6a47f5739962a schema:name Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Université de Strasbourg, Strasbourg 67000, France
112 rdf:type schema:Organization
113 N7c5be15f4dbf48ac9a7fca091a4d9483 schema:name Springer Nature - SN SciGraph project
114 rdf:type schema:Organization
115 N802718abbfea4917b0a567eb27ada2fb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Protein Biosynthesis
117 rdf:type schema:DefinedTerm
118 N8c1ee74c49204076b8de389bb9e40cc9 rdf:first sg:person.01313146525.30
119 rdf:rest rdf:nil
120 N8f6ef066b300455eba8141fe2d53ac99 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
121 schema:name Models, Genetic
122 rdf:type schema:DefinedTerm
123 N9730fced215a4ae5865796565cf95de5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Models, Molecular
125 rdf:type schema:DefinedTerm
126 N9ace2ee0ef88413da88c58b9b441f137 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name RNA, Messenger
128 rdf:type schema:DefinedTerm
129 N9eaefc9b3b9342299575da6ee489b94d schema:name pubmed_id
130 schema:value 22437501
131 rdf:type schema:PropertyValue
132 Na5ba74b9d29245498307af2f4febdc73 rdf:first sg:person.0576270133.74
133 rdf:rest Nf68073ebfc3a4921acf1bdf5436b6c3e
134 Naae17696af594d75acd9a0b8ca4ec50e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
135 schema:name Protein Conformation
136 rdf:type schema:DefinedTerm
137 Nbff9f241871b41cca19d96647e2b2ff6 rdf:first sg:person.01232312222.62
138 rdf:rest Na5ba74b9d29245498307af2f4febdc73
139 Nc212ca8a58e2481482037dcc13bd8ff9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
140 schema:name Models, Biological
141 rdf:type schema:DefinedTerm
142 Nc54fcfaba3d647b5be19794e71910422 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Nucleic Acid Conformation
144 rdf:type schema:DefinedTerm
145 Nc9a992f776664b98bbc25f0490dfd820 schema:issueNumber 7393
146 rdf:type schema:PublicationIssue
147 Ncc735fd81e73402a865419e5d66a1e0a schema:volumeNumber 484
148 rdf:type schema:PublicationVolume
149 Ndae76cf7229b4c94b91eaa76779278ef schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
150 schema:name Crystallography, X-Ray
151 rdf:type schema:DefinedTerm
152 Ne1b3f5ffdc644154a551ea6974c7675e schema:name Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; CNRS, UMR7104, Illkirch 67400, France; INSERM, U964, Illkirch 67400, France; Université de Strasbourg, Strasbourg 67000, France
153 rdf:type schema:Organization
154 Ne5da4268c08446749e8dece47363d8e1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
155 schema:name RNA, Ribosomal, 23S
156 rdf:type schema:DefinedTerm
157 Ne885b52ff2ea4a0db82236d490f8b2ac schema:name dimensions_id
158 schema:value pub.1022866252
159 rdf:type schema:PropertyValue
160 Nf68073ebfc3a4921acf1bdf5436b6c3e rdf:first sg:person.01242346450.12
161 rdf:rest N461366bef3d5474eb8dc3b6fc5659ace
162 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
163 schema:name Biological Sciences
164 rdf:type schema:DefinedTerm
165 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
166 schema:name Biochemistry and Cell Biology
167 rdf:type schema:DefinedTerm
168 sg:grant.3786087 http://pending.schema.org/fundedItem sg:pub.10.1038/nature10913
169 rdf:type schema:MonetaryGrant
170 sg:journal.1018957 schema:issn 0090-0028
171 1476-4687
172 schema:name Nature
173 rdf:type schema:Periodical
174 sg:person.01232312222.62 schema:affiliation N10eb8c9d043d4f97896cbc9851e75026
175 schema:familyName Demeshkina
176 schema:givenName Natalia
177 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232312222.62
178 rdf:type schema:Person
179 sg:person.01242346450.12 schema:affiliation https://www.grid.ac/institutes/grid.465534.5
180 schema:familyName Westhof
181 schema:givenName Eric
182 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242346450.12
183 rdf:type schema:Person
184 sg:person.01313146525.30 schema:affiliation Ne1b3f5ffdc644154a551ea6974c7675e
185 schema:familyName Yusupova
186 schema:givenName Gulnara
187 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01313146525.30
188 rdf:type schema:Person
189 sg:person.0576270133.74 schema:affiliation N26c7db4a929d4f1e88e8691322ac5179
190 schema:familyName Jenner
191 schema:givenName Lasse
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0576270133.74
193 rdf:type schema:Person
194 sg:person.0773543020.27 schema:affiliation N75f313d54814468ab4c6a47f5739962a
195 schema:familyName Yusupov
196 schema:givenName Marat
197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773543020.27
198 rdf:type schema:Person
199 sg:pub.10.1038/72364 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033232899
200 https://doi.org/10.1038/72364
201 rdf:type schema:CreativeWork
202 sg:pub.10.1038/nsmb.1577 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007018540
203 https://doi.org/10.1038/nsmb.1577
204 rdf:type schema:CreativeWork
205 sg:pub.10.1038/nsmb.1790 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008900126
206 https://doi.org/10.1038/nsmb.1790
207 rdf:type schema:CreativeWork
208 sg:pub.10.1038/nsmb.1880 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027212590
209 https://doi.org/10.1038/nsmb.1880
210 rdf:type schema:CreativeWork
211 sg:pub.10.1038/nsmb.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022046953
212 https://doi.org/10.1038/nsmb.2003
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1016/0022-2836(90)90016-f schema:sameAs https://app.dimensions.ai/details/publication/pub.1017742608
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1016/j.cell.2009.01.036 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006013070
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1016/j.febslet.2004.11.048 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027764924
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1016/j.jmb.2010.04.038 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022144736
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1016/j.molcel.2005.12.018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049853767
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1016/j.tibs.2005.10.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040890497
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1016/s0022-2836(05)80023-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041097615
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1016/s0092-8674(02)01086-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049702328
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1016/s0300-9084(86)80023-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030456101
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1017/s1355838201002382 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054923649
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1038/emboj.2008.243 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048490262
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1038/emboj.2009.26 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032259085
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1073/pnas.0705988104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053587492
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1073/pnas.1012825108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036625209
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1107/s0907444909021933 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038618493
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1107/s0907444909052925 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020777046
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1107/s0907444911049833 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023977440
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1126/science.1060612 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002395498
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1126/science.1111408 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029815934
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1126/science.1131127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003901838
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1126/science.1179700 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062460594
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1126/science.1194460 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040923975
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1126/science.285.5434.1722 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062566569
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1146/annurev.biochem.70.1.415 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029650829
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1261/rna.2035410 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000810396
263 rdf:type schema:CreativeWork
264 https://www.grid.ac/institutes/grid.465534.5 schema:alternateName Institute for Molecular and Cellular Biology
265 schema:name Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg 67084, France
266 rdf:type schema:Organization
 




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


...