4ZBY image
Deposition Date 2015-04-15
Release Date 2015-09-09
Last Version Date 2023-11-08
Entry Detail
PDB ID:
4ZBY
Keywords:
HYDROLASE
Title:
Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (uracil complex form)
Biological Source:
Source Organism:
Sulfolobus tokodaii str. 7 (Taxon ID: 273063)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.70 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
4ZBY validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uracil-DNA glycosylase
Gene (Uniprot):STK_22380
Chain IDs:A
Chain Length:194
Number of Molecules:1
Biological Source:Sulfolobus tokodaii str. 7
UniProt ID:Q96YD0 Pfam ID:PF03167 EC:3.2.2.27
Ligand Molecules
MES
SF4
URA
Primary Citation
Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding
Febs Lett. 589 2675 2682 (2015)
PMID: 26318717 DOI: 10.1016/j.febslet.2015.08.019

Abstact

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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Chemical

Disease

Primary Citation of related structures
4ZBX
4ZBZ