3AAL

Crystal Structure of endonuclease IV from Geobacillus kaustophilus

• PDB DOI: https://doi.org/10.2210/pdb3AAL/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus kaustophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-20 Released: 2010-12-01 
• Deposition Author(s): Asano, R., Ishikawa, H., Nakane, S., Nakagawa, N., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 21358045 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.82 kDa 
• Atom Count: 2,434 
• Modelled Residue Count: 298 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable endonuclease 4	A	303	Geobacillus kaustophilus	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	B [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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 = 85.17	α = 90
b = 85.17	β = 90
c = 140.22	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Asano, R., Ishikawa, H., Nakane, S., Nakagawa, N., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description