Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.17 kDa 
• Atom Count: 1129 
• Modelled Residue Count: 133 
• Deposited Residue Count: 143 
• Unique protein chains: 1

1J25

Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain, Mn cocrystal

• PDB DOI: 10.2210/pdb1J25/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-12-25 Released: 2003-04-22 
• Deposition Author(s): Nishino, T., Komori, K., Ishino, Y., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.252 
• R-Value Work: 0.228 

Literature

X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes

Nishino, T., Komori, K., Ishino, Y., Morikawa, K.

(2003) Structure 11: 445-457

• PubMed: 12679022 
• DOI: 10.1016/s0969-2126(03)00046-7
• Primary Citation of Related Structures:  
  1J22, 1J23, 1J24, 1J25


• PubMed Abstract: 
  

The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. Here, we report the domain organization of an archaeal homolog (Hef) of this family and the X-ray crystal structure of the middle domain, with the nuclease activity. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases, including the correspondence of the GDX(n)ERKX(3)D signature motif in Hef to the PDX(n)(E/D)XK motif in restriction enzymes. This structural study also suggests that the XPF/Rad1/Mus81/ERCC1 proteins form a dimer through each interface of the nuclease domain and the helix-hairpin-helix domain. Simultaneous disruptions of both interfaces result in their dissociation into separate monomers, with strikingly reduced endonuclease activities.

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Organizational Affiliation: 

Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, 565-0874, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase, putative	A	143	Pyrococcus furiosus DSM 3638	Mutation(s): 2  Gene Names: PF2015
UniProt
Find proteins for Q8TZH8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZH8  Go to UniProtKB:  Q8TZH8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.252 
• R-Value Work: 0.228 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.795	α = 90
b = 69.795	β = 90
c = 58.509	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-25 
• Released Date: 2003-04-22 
Deposition Author(s): Nishino, T., Komori, K., Ishino, Y., Morikawa, K.

Revision History  

• Version 1.0: 2003-04-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations