4ZBZ | pdb_00004zbz

Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)

• PDB DOI: https://doi.org/10.2210/pdb4ZBZ/pdb

• Classification: HYDROLASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-15 Released: 2015-09-09 
• Deposition Author(s): Kawai, A., Miyamoto, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding

Kawai, A., Higuchi, S., Tsunoda, M., Nakamura, K.T., Yamagata, Y., Miyamoto, S.

(2015) FEBS Lett 589: 2675-2682

• PubMed: 26318717 
• DOI: https://doi.org/10.1016/j.febslet.2015.08.019
• Primary Citation Related Structures: 
  4ZBX, 4ZBY, 4ZBZ


• PubMed Abstract: 
  

  Uracil-DNA glycosylases (UDGs) excise uracil from DNA by catalyzing the N-glycosidic bond hydrolysis. Here we report the first crystal structures of an archaeal UDG (stoUDG). Compared with other UDGs, stoUDG has a different structure of the leucine-intercalation loop, which is important for DNA binding. The stoUDG-DNA complex model indicated that Leu169, Tyr170, and Asn171 in the loop are involved in DNA intercalation. Mutational analysis showed that Tyr170 is critical for substrate DNA recognition. These results indicate that Tyr170 occupies the intercalation site formed after the structural change of the leucine-intercalation loop required for the catalysis.

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Organizational Affiliation: 
• Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan. Electronic address: [e-mail].
Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.
Faculty of Pharmacy, Iwaki Meisei University, 5-5-1 Chuodai-iino, Iwaki 970-8551, Japan.
School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan.
Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.

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: 23 kDa 
• Atom Count: 1,854 
• Modeled Residue Count: 192 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	194	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: STK_22380 EC: 3.2.2.27
UniProt
Find proteins for Q96YD0 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96YD0  Go to UniProtKB:  Q96YD0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.03	α = 90
b = 52.345	β = 90
c = 74.689	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Kawai, A., Miyamoto, S.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Database references
• Version 1.2: 2015-09-23
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description