Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.55 kDa 
• Atom Count: 2,553 
• Modelled Residue Count: 267 
• Deposited Residue Count: 274 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 2DNJ

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

• PDB DOI:  https://doi.org/10.2210/pdb2DNJ/pdb
• NDB: PDE006

• Classification: HYDROLASE/DNA
• Organism(s): Bos taurus
• Mutation(s): No 


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

---

Experimental Data Snapshot

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

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

• PubMed: 1748997 
• DOI: https://doi.org/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. 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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYRIBONUCLEASE I	C [auth A]	260	Bos taurus	Mutation(s): 0  Gene Names: DNASE1, DNL1 EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus) Explore P00639  Go to UniProtKB:  P00639

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'	A [auth B]	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*TP*C)-3'	B [auth C]	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 72.9	α = 90
b = 100.1	β = 90
c = 92.6	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• 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
• 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