2VLD | pdb_00002vld

crystal structure of a repair endonuclease from Pyrococcus abyssi

• PDB DOI: https://doi.org/10.2210/pdb2VLD/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-01-14 Released: 2009-05-19 
• Deposition Author(s): Ren, B., Kuhn, J., Meslet-Cladiere, L., Briffotaux, J., Norais, C., Lavigne, R., Flament, D., Ladenstein, R., Myllykallio, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.248 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

Structure and function of a novel endonuclease acting on branched DNA substrates.

Ren, B., Kuhn, J., Meslet-Cladiere, L., Briffotaux, J., Norais, C., Lavigne, R., Flament, D., Ladenstein, R., Myllykallio, H.

(2009) EMBO J 28: 2479-2489

• PubMed: 19609302 
• DOI: https://doi.org/10.1038/emboj.2009.192
• Primary Citation Related Structures: 
  2VLD


• PubMed Abstract: 
  

  We show that Pyrococcus abyssi PAB2263 (dubbed NucS (nuclease for ss DNA) is a novel archaeal endonuclease that interacts with the replication clamp PCNA. Structural determination of P. abyssi NucS revealed a two-domain dumbbell-like structure that in overall does not resemble any known protein structure. Biochemical and structural studies indicate that NucS orthologues use a non-catalytic ssDNA-binding domain to regulate the cleavage activity at another site, thus resulting into the specific cleavage at double-stranded DNA (dsDNA)/ssDNA junctions on branched DNA substrates. Both 3' and 5' extremities of the ssDNA can be cleaved at the nuclease channel that is too narrow to accommodate duplex DNA. Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis.

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Organizational Affiliation: 
• Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 58.3 kDa 
• Atom Count: 3,791 
• Modeled Residue Count: 454 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease NucS	A, B	251	Pyrococcus abyssi	Mutation(s): 2  Gene Names: nucS, PYRAB01260, PAB2263 EC: 3.1
UniProt
Find proteins for Q9V2E8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2E8  Go to UniProtKB:  Q9V2E8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.248 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.966	α = 90
b = 100.688	β = 90
c = 157.686	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Ren, B., Kuhn, J., Meslet-Cladiere, L., Briffotaux, J., Norais, C., Lavigne, R., Flament, D., Ladenstein, R., Myllykallio, H.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-09-26
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary