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: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.239 

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

  • 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 conserv ...

    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: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Intron-encoded endonuclease I-AniI
Z
254Emericella nidulansMutation(s): 0 
Gene Names: I-AniI
Find proteins for P03880 (Emericella nidulans)
Go to UniProtKB:  P03880
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3'A18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3'B13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3'C16N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3'D15N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
Z
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.462α = 90.00
b = 72.841β = 108.21
c = 65.231γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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