3TC3

Crystal Structure of SacUVDE

• PDB DOI:  https://doi.org/10.2210/pdb3TC3/pdb

• Classification: HYDROLASE
• Organism(s): Sulfolobus acidocaldarius DSM 639
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-08 Released: 2012-11-07 
• Deposition Author(s): Meulenbroek, E.M., Jala, I., Moolenaar, G.F., Goosen, N., Pannu, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.214 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions.

Meulenbroek, E.M., Peron Cane, C., Jala, I., Iwai, S., Moolenaar, G.F., Goosen, N., Pannu, N.S.

(2013) Nucleic Acids Res 41: 1363-1371

• PubMed: 23221644 
• DOI: https://doi.org/10.1093/nar/gks1127
• Primary Citation of Related Structures:  
  3TC3, 4GLE


• PubMed Abstract: 
  

Repairing damaged DNA is essential for an organism's survival. UV damage endonuclease (UVDE) is a DNA-repair enzyme that can recognize and incise different types of damaged DNA. We present the structure of Sulfolobus acidocaldarius UVDE on its own and in a pre-catalytic complex with UV-damaged DNA containing a 6-4 photoproduct showing a novel 'dual dinucleotide flip' mechanism for recognition of damaged dipyrimidines: the two purines opposite to the damaged pyrimidine bases are flipped into a dipurine-specific pocket, while the damaged bases are also flipped into another cleft.

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Organizational Affiliation: 

Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.51 kDa 
• Atom Count: 5,285 
• Modelled Residue Count: 579 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UV damage endonuclease	A, B	310	Sulfolobus acidocaldarius DSM 639	Mutation(s): 0  Gene Names: uvdE, Saci_1096 EC: 3
UniProt
Find proteins for Q4J9T1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4J9T1  Go to UniProtKB:  Q4J9T1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.214 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.075	α = 102.1
b = 53.585	β = 93.02
c = 77.395	γ = 111.77

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Meulenbroek, E.M., Jala, I., Moolenaar, G.F., Goosen, N., Pannu, N.S.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2012-12-26
  Changes: Database references
• Version 1.3: 2013-02-06
  Changes: Database references
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description