4GLE

SacUVDE in complex with 6-4PP-containing DNA

• PDB DOI: https://doi.org/10.2210/pdb4GLE/pdb
• NAKB: 4GLE

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


• Deposited: 2012-08-14 Released: 2012-11-21 
• Deposition Author(s): Meulenbroek, E.M., Peron Cane, C., Jala, I., Iwai, S., Moolenaar, G.F., Goosen, N., Pannu, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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)

Macromolecule Content

• Total Structure Weight: 45.07 kDa 
• Atom Count: 2,976 
• Modelled Residue Count: 322 
• Deposited Residue Count: 340 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UV damage endonuclease	C [auth A]	310	Sulfolobus acidocaldarius	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*TP*CP*GP*TP*CP*AP*AP*GP*GP*AP*CP*GP*C)-3'	A [auth B]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*CP*CP*(64T)P*(5PY)P*GP*AP*CP*GP*AP*CP*G)-3'	B [auth C]	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.2	α = 90
b = 112.51	β = 90
c = 153.85	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Meulenbroek, E.M., Peron Cane, C., Jala, I., Iwai, S., Moolenaar, G.F., Goosen, N., Pannu, N.S.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2012-12-26
  Changes: Database references
• Version 1.2: 2013-02-06
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary