2DNJ

DNASE I-INDUCED DNA CONFORMATION. 2 ANGSTROMS STRUCTURE OF A DNASE I-OCTAMER COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex

Lahm, A.Suck, D.

(1991) J Mol Biol 222: 645-667

  • DOI: 10.1016/0022-2836(91)90502-w
  • Primary Citation of Related Structures:  
    2DNJ

  • PubMed Abstract: 
  • The structure of a complex between DNase I and d(GCGATCGC)2 has been solved by molecular replacement and refined to an R-factor of 0.174 for all data between 6 and 2 A resolution. The nicked octamer duplexes have lost a dinucleotide from the 3' ends of one strand and are hydrogen-bonded across a 2-fold axis to form a quasi-continuous double helix of 14 base-pairs ...

    The structure of a complex between DNase I and d(GCGATCGC)2 has been solved by molecular replacement and refined to an R-factor of 0.174 for all data between 6 and 2 A resolution. The nicked octamer duplexes have lost a dinucleotide from the 3' ends of one strand and are hydrogen-bonded across a 2-fold axis to form a quasi-continuous double helix of 14 base-pairs. DNase I is bound in the minor groove of the B-type DNA duplex forming contacts in and along both sides of the minor groove extending over a total of six base-pairs. As a consequence of binding of DNase I to the DNA-substrate the minor groove opens by about 3 A and the duplex bends towards the major groove by about 20 degrees. Apart from these more global distortions the bound duplex also shows significant deviations in local geometry. A major cause for the observed perturbations in the DNA conformation seems to be the stacking type interaction of a tyrosine ring (Y76) with a deoxyribose. In contrast, the enzyme structure is nearly unchanged compared to free DNase I (0.49 A root-mean-square deviations for main-chain atoms) thus providing a rigid framework to which the DNA substrate has to adapt on binding. These results confirm the hypothesis that groove width and stiffness are major factors determining the global sequence dependence of the enzyme's cutting rates. The nicked octamer present in the crystals did not allow us to draw detailed conclusions about the catalytic mechanism but confirmed the location of the active site near H134 on top of the central beta-sheets. A second cut of the DNA induced by diffusion of Mn2+ into the crystals may suggest the presence of a secondary active site in DNase I.


    Related Citations: 
    • Structure Refined to 2 Angstroms of a Nicked DNA Octanucleotide Complex with DNase I
      Suck, D., Lahm, A., Oefner, C.
      (1988) Nature 332: 465
    • Structure of DNase I at 2.0 Angstroms Resolution Suggests a Mechanism for Binding to and Cutting DNA
      Suck, D., Oefner, C.
      (1986) Nature 321: 620
    • Three-Dimensional Structure of Bovine Pancreatic DNase I at 2.5 Angstroms Resolution
      Suck, D., Oefner, C., Kabsch, W.
      (1984) EMBO J 3: 2423
    • Crystallization and Preliminary Crystallographic Data of Bovine Pancreatic Deoxyribonuclease I
      Suck, D.
      (1982) J Mol Biol 162: 511
    • Bovine Pancreatic Deoxyribonuclease A. Isolation of Cyanogen Bromide Peptides, Complete Covalent Structure of the Polypeptide Chain
      Liao, T.-H., Salnikow, J., Moore, S., Stein, W.H.
      (1973) J Biol Chem 248: 1489

    Organizational Affiliation

    European Molecular Biology Laboratory, Biological Structures Division, Heidelberg, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DEOXYRIBONUCLEASE IC [auth A]260Bos taurusMutation(s): 0 
Gene Names: DNASE1DNL1
EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus)
Explore P00639 
Go to UniProtKB:  P00639
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'A [auth B]8N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*GP*AP*TP*C)-3'B [auth C]6N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      NAG (Subject of Investigation/LOI)
      Query on NAG

      Download Ideal Coordinates CCD File 
      D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
      C8 H15 N O6
      OVRNDRQMDRJTHS-FMDGEEDCSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Observed: 0.174 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 72.9α = 90
      b = 100.1β = 90
      c = 92.6γ = 90
      Software Package:
      Software NamePurpose
      PROLSQrefinement

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      • Deposited Date: 1986-10-21 
      • Released Date: 1994-01-31 
      • Deposition Author(s): Lahm, A., Suck, D.

      Revision History  (Full details and data files)

      • Version 1.0: 1994-01-31
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2017-11-29
        Changes: Derived calculations
      • Version 1.4: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Data collection, Derived calculations, Structure summary
      • Version 2.0: 2020-10-21
        Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary