1P8K

The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.

Bolduc, J.M.Spiegel, P.C.Chatterjee, P.Brady, K.L.Downing, M.E.Caprara, M.G.Waring, R.B.Stoddard, B.L.

(2003) Genes Dev 17: 2875-2888

  • DOI: 10.1101/gad.1109003
  • Primary Citation of Related Structures:  
    1P8K

  • PubMed Abstract: 
  • We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 A resolution. The structure demonstrates the remarkable structural conservation of the beta-sheet DNA-binding motif between highly divergent enzyme subfamilies ...

    We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 A resolution. The structure demonstrates the remarkable structural conservation of the beta-sheet DNA-binding motif between highly divergent enzyme subfamilies. DNA recognition by I-AniI was further studied using nucleoside deletion and DMS modification interference analyses. Correlation of these results with the crystal structure provides information on the relative importance of individual nucleotide contacts for DNA recognition. Alignment and modeling of two homologous maturases reveals conserved basic surface residues, distant from the DNA-binding surface, that might be involved in RNA binding. A point mutation that introduces a single negative charge in this region uncouples the maturase and endonuclease functions of the protein, inhibiting RNA binding and splicing while maintaining DNA binding and cleavage.


    Organizational Affiliation

    Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, Washington 98109, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-encoded endonuclease I-AniIE [auth Z]254Aspergillus nidulansMutation(s): 2 
Gene Names: Aspergillus nidulansI-AniI
EC: 3.1
UniProt
Find proteins for P03880 (Emericella nidulans)
Explore P03880 
Go to UniProtKB:  P03880
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3'A18N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3'B13N/A
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3'C16N/A
        Protein Feature View
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        • Reference Sequence
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
          MoleculeChainsLengthOrganismImage
          5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3'D15N/A
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 1 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          F [auth B], G [auth Z]MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Modified Residues  1 Unique
          IDChainsTypeFormula2D DiagramParent
          MSE
          Query on MSE
          E [auth Z]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
          Binding Affinity Annotations 
          IDSourceBinding Affinity
          DNA PDBBind:  1P8K Kd: 11 (nM) from 1 assay(s)
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 2.60 Å
          • R-Value Free: 0.264 
          • R-Value Work: 0.239 
          • R-Value Observed: 0.247 
          • Space Group: P 1 21 1
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 60.462α = 90
          b = 72.841β = 108.21
          c = 65.231γ = 90
          Software Package:
          Software NamePurpose
          HKL-2000data collection
          SCALEPACKdata scaling
          CNSrefinement
          HKL-2000data reduction
          CNSphasing

          Structure Validation

          View Full Validation Report




          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2004-01-20
            Type: Initial release
          • Version 1.1: 2008-04-29
            Changes: Version format compliance
          • Version 1.2: 2011-07-13
            Changes: Version format compliance