3BO2

A relaxed active site following exon ligation by a group I intron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.292 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A relaxed active site after exon ligation by the group I intron

Lipchock, S.V.Strobel, S.A.

(2008) Proc Natl Acad Sci U S A 105: 5699-5704

  • DOI: 10.1073/pnas.0712016105
  • Primary Citation of Related Structures:  
    3BO2, 3BO3, 3BO4

  • PubMed Abstract: 
  • During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing ...

    During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.


    Organizational Affiliation

    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AE [auth A]95Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Group I intron P9A [auth B]197synthetic construct
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*G)-3')B [auth C]16synthetic construct
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*AP*CP*GP*GP*CP*C)-3')C [auth D]6synthetic construct
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        RNA (5'-R(*CP*AP*U)-3')D [auth E]3synthetic construct
        Protein Feature View
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        • Reference Sequence
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 3.31 Å
        • R-Value Free: 0.321 
        • R-Value Work: 0.291 
        • R-Value Observed: 0.292 
        • Space Group: P 41 2 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 108.96α = 90
        b = 108.96β = 90
        c = 249.495γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        REFMACrefinement
        PDB_EXTRACTdata extraction

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2008-04-01
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance
        • Version 1.2: 2017-10-25
          Changes: Refinement description, Source and taxonomy