1DNK

THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.

Weston, S.A.Lahm, A.Suck, D.

(1992) J.Mol.Biol. 226: 1237-1256


  • PubMed Abstract: 
  • The crystal structure of a complex between DNase I and the self-complementary octamer duplex d(GGTATACC)2 has been solved using the molecular replacement method and refined to a crystallographic R-factor of 18.8% for all data between 6.0 and 2.3 A re ...

    The crystal structure of a complex between DNase I and the self-complementary octamer duplex d(GGTATACC)2 has been solved using the molecular replacement method and refined to a crystallographic R-factor of 18.8% for all data between 6.0 and 2.3 A resolution. In contrast to the structure of the DNase I-d(GCGATCGC)2 complex solved previously, the DNA remains uncleaved in the crystal. The general architecture of the two complexes is highly similar. DNase I binds in the minor groove of a right-handed DNA duplex, and to the phosphate backbones on either side over five base-pairs, resulting in a widening of the minor groove and a concurrent bend of the DNA away from the bound enzyme. There is very little change in the structure of the DNase I on binding the substrate. Many other features of the interaction are conserved in the two complexes, in particular the stacking of a deoxyribose group of the DNA onto the side-chain of a tyrosine residue (Y76), which affects the DNA conformation and the binding of an arginine side-chain in the minor groove. Although the structures of the DNA molecules appear at first sight rather similar, detailed analysis reveals some differences that may explain the relative resistance of the d(GGTATACC)2 duplex to cleavage by DNase I: whilst some backbone parameters are characteristic of a B-conformation, the spatial orientation of the base-pairs in the d(GGTATACC)2 duplex is close to that generally observed in A-DNA. These results further support the hypothesis that the minor-groove width and depth and the intrinsic flexibility of DNA are the most important parameters affecting the interaction. The disposition of residues around the scissile phosphate group suggests that two histidine residues, H134 and H252, are involved in catalysis.


    Related Citations: 
    • 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
    • Crystallographic refinement and structure of DNAse I at 2 Angstroms resolution
      Oefner, C.,Suck, D.
      (1986) J.Mol.Biol. 192: 605
    • DNAse I induced DNA conformation: 2 Angstroms structure of a DNAse-octamer complex
      Lahm, A.,Suck, D.
      (1991) J.Mol.Biol. 222: 645
    • 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
    • Structure refined to 2 Angstroms of a nicked DNA octanucleotide complex with DNAse I
      Suck, D.,Lahm, A.,Oefner, C.
      (1988) Nature 332: 465
    • Crystallization and preliminary crystallographic data of bovine pancreatic deoxyribonuclease I
      Suck, D.
      (1982) J.Mol.Biol. 162: 511
    • Three-dimensional structure of bovine pancreatic DNAse I at 2.5 Angstroms resolution
      Suck, D.,Oefner, C.,Kabsch, W.
      (1984) Embo J. 3: 2423


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))
A
260Bos taurusMutation(s): 0 
Gene Names: DNASE1 (DNL1)
EC: 3.1.21.1
Find proteins for P00639 (Bos taurus)
Go to Gene View: DNASE1
Go to UniProtKB:  P00639
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3')B7N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3')C8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.100α = 90.00
b = 108.400β = 90.00
c = 62.100γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance