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: 2.30 Å
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • DOI: 10.1016/0022-2836(92)91064-v
  • Primary Citation of Related Structures:  
    1DNK

  • 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 resolution ...

    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: 
    • DNAse I induced DNA conformation: 2 Angstroms structure of a DNAse-octamer complex
      Lahm, A., Suck, D.
      (1991) J Mol Biol 222: 645
    • 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
    • Crystallographic refinement and structure of DNAse I at 2 Angstroms resolution
      Oefner, C., Suck, D.
      (1986) J Mol Biol 192: 605
    • 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

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))C [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
Entity Groups  
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UniProt GroupP00639
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3')A [auth B]7N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3')B [auth C]8N/A
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.1α = 90
b = 108.4β = 90
c = 62.1γ = 90
Software Package:
Software NamePurpose
TNTrefinement
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

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: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary