1IAW

CRYSTAL STRUCTURE OF NAEI COMPLEXED WITH 17MER DNA

• PDB DOI: https://doi.org/10.2210/pdb1IAW/pdb
• NAKB: 1IAW

• Classification: HYDROLASE/DNA
• Organism(s): Lentzea aerocolonigenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-03-23 Released: 2001-08-03 
• Deposition Author(s): Huai, Q., Colandene, J.D., Topal, M.D., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.293 
• R-Value Work: 0.243 

Literature

Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement.

Huai, Q., Colandene, J.D., Topal, M.D., Ke, H.

(2001) Nat Struct Biol 8: 665-669

• PubMed: 11473254 
• DOI: https://doi.org/10.1038/90366
• Primary Citation of Related Structures:  
  1IAW


• PubMed Abstract: 
  

  NaeI, a novel DNA endonuclease, shows topoisomerase and recombinase activities when a Lys residue is substituted for Leu 43. The NaeI-DNA structure demonstrates that each of the two domains of NaeI recognizes one molecule of DNA duplex. DNA recognition induces dramatic rearrangements: narrowing the binding site of the Topo domain 16 A to grip DNA, widening that of the Endo domain 8 A to encircle and bend DNA 45 degrees for cleavage, and completely rebuilding the homodimer interface. The NaeI-DNA structure presents the first example of novel recognition of two copies of one DNA sequence by two different amino acid sequences and two different structural motifs in one polypeptide.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.59 kDa 
• Atom Count: 6,195 
• Modelled Residue Count: 675 
• Deposited Residue Count: 702 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE II RESTRICTION ENZYME NAEI	E [auth A], F [auth B]	317	Lentzea aerocolonigenes	Mutation(s): 0  Gene Names: NAE I EC: 3.1.21.4
UniProt
Find proteins for P50187 (Lentzea aerocolonigenes) Explore P50187  Go to UniProtKB:  P50187

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*GP*GP*C)-3'	A [auth C], B [auth D], C [auth E], D [auth F]	17	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.293 
• R-Value Work: 0.243 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.6	α = 90
b = 65	β = 90
c = 258.5	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-08-03 
Deposition Author(s): Huai, Q., Colandene, J.D., Topal, M.D., Ke, H.

Revision History  

• Version 1.0: 2001-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-07-25
  Changes: Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description