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 1.3 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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DEOXYRIBONUCLEASE I
A
260Bos taurusMutation(s): 0 
Gene Names: DNASE1DNL1
EC: 3.1.21.1
Find proteins for P00639 (Bos taurus)
Go to UniProtKB:  P00639
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'B8N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*AP*TP*C)-3'C6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGA
Query on NGA

Download CCD File 
A
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-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 

  • 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