3AAL

Crystal Structure of endonuclease IV from Geobacillus kaustophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 

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This is version 1.3 of the entry. See complete history. 


Literature

An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA

Asano, R., Ishikawa, H., Nakane, S., Nakagawa, N., Kuramitsu, S., Masui, R.

(2011) Acta Crystallogr D Biol Crystallogr 67: 149-155

  • DOI: 10.1107/S0907444910052479
  • Primary Citation of Related Structures:  
    3AAL, 3AAM

  • PubMed Abstract: 

    • Endonuclease IV (EndoIV) is an endonuclease that acts at apurinic/apyrimidinic (AP) sites and is classified as either long-type or short-type. The crystal structures of representative types of EndoIV from Geobacillus kaustophilus and Thermus thermophilus HB8 were determined using X-ray crystallography ...

    Endonuclease IV (EndoIV) is an endonuclease that acts at apurinic/apyrimidinic (AP) sites and is classified as either long-type or short-type. The crystal structures of representative types of EndoIV from Geobacillus kaustophilus and Thermus thermophilus HB8 were determined using X-ray crystallography. G. kaustophilus EndoIV (the long type) had a higher affinity for double-stranded DNA containing an AP-site analogue than T. thermophilus EndoIV (the short type). Structural analysis of the two different EndoIVs suggested that a C-terminal DNA-recognition loop that is only present in the long type contributes to its high affinity for AP sites. A mutation analysis showed that Lys267 in the C-terminal DNA-recognition loop plays an important role in DNA binding.

    Organizational Affiliation: 

    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable endonuclease 4A303Geobacillus kaustophilusMutation(s): 0 
Gene Names: GK2474
EC: 3.1.21.2
UniProt
Find proteins for Q5KX27 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KX27 
Go to UniProtKB:  Q5KX27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KX27
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC
Download Ideal Coordinates CCD File 
B [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
FE
Query on FE
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.17α = 90
b = 85.17β = 90
c = 140.22γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description