1U3E

DNA binding and cleavage by the HNH homing endonuclease I-HmuI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI.

Shen, B.W.Landthaler, M.Shub, D.A.Stoddard, B.L.

(2004) J Mol Biol 342: 43-56

  • DOI: 10.1016/j.jmb.2004.07.032
  • Primary Citation of Related Structures:  
    1U3E

  • PubMed Abstract: 
  • The structure of I-HmuI, which represents the last family of homing endonucleases without a defining crystallographic structure, has been determined in complex with its DNA target. A series of diverse protein structural domains and motifs, contacting ...

    The structure of I-HmuI, which represents the last family of homing endonucleases without a defining crystallographic structure, has been determined in complex with its DNA target. A series of diverse protein structural domains and motifs, contacting sequential stretches of nucleotide bases, are distributed along the DNA target. I-HmuI contains an N-terminal domain with a DNA-binding surface found in the I-PpoI homing endonuclease and an associated HNH/N active site found in the bacterial colicins, and a C-terminal DNA-binding domain previously observed in the I-TevI homing endonuclease. The combination and exchange of these features between protein families indicates that the genetic mobility associated with homing endonucleases extends to the level of independent structural domains. I-HmuI provides an unambiguous structural connection between the His-Cys box endonucleases and the bacterial colicins, supporting the hypothesis that these enzymes diverged from a common ancestral nuclease.


    Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. A3-025, Seattle, WA 98109, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HNH homing endonucleaseM174Bacillus virus SPO1Mutation(s): 0 
Gene Names: bacteriophage SP01
EC: 3.1
Find proteins for P34081 (Bacillus phage SP01)
Explore P34081 
Go to UniProtKB:  P34081
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
36-MERA36N/A
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3'B21N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'C15N/A
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TRS
    Query on TRS

    Download CCD File 
    M
    2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
    C4 H12 N O3
    LENZDBCJOHFCAS-UHFFFAOYSA-O
     Ligand Interaction
    SR
    Query on SR

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    A, M
    STRONTIUM ION
    Sr
    PWYYWQHXAPXYMF-UHFFFAOYSA-N
     Ligand Interaction
    EDO
    Query on EDO

    Download CCD File 
    A, B, C, M
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    MN
    Query on MN

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    M
    MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.92 Å
    • R-Value Free: 0.247 
    • R-Value Work: 0.216 
    • R-Value Observed: 0.220 
    • Space Group: I 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 45α = 90
    b = 108.3β = 90
    c = 248.1γ = 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 

    • Version 1.0: 2004-08-31
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2011-11-16
      Changes: Atomic model