Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 58303.80 
• Atom Count: 3679 
• Residue Count: 502 
• Unique protein chains: 1

2VLD

crystal structure of a repair endonuclease from Pyrococcus abyssi

• DOI: 10.2210/pdb2VLD/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus abyssi (strain GE5 / Orsay)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• 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: 2.6 Å
• R-Value Free: 0.248 
• R-Value Work: 0.243 

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: 10.1038/emboj.2009.192


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Endonuclease NucS	A, B	251	Pyrococcus abyssi (strain GE5 / Orsay)	Mutation(s): 2  Gene Names: nucS EC: 3.1.-.-
Find proteins for Q9V2E8 (Pyrococcus abyssi (strain GE5 / Orsay)) 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: 2.6 Å
• R-Value Free: 0.248 
• R-Value Work: 0.243 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 78.966	α = 90.00
b = 100.688	β = 90.00
c = 157.686	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-14 
• 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
  Type: Advisory, Version format compliance
• Version 1.2: 2018-09-26
  Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary