4zby

From Proteopedia

Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (uracil complex form)

PDB ID 4zby

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Structural highlights

4zby is a 1 chain structure with sequence from Sulfurisphaera tokodaii str. 7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UDGA_SULTO Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP.^[1]

Publication Abstract from PubMed

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.

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 KT, Yamagata Y, Miyamoto S FEBS Lett. 2015 Sep 14;589(19 Pt B):2675-82. doi: 10.1016/j.febslet.2015.08.019. , Epub 2015 Aug 28. PMID:26318717^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Yamagata Y, Miyamoto S. Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding. FEBS Lett. 2015 Sep 14;589(19 Pt B):2675-82. doi: 10.1016/j.febslet.2015.08.019. , Epub 2015 Aug 28. PMID:26318717 doi:http://dx.doi.org/10.1016/j.febslet.2015.08.019
↑ Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Yamagata Y, Miyamoto S. Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding. FEBS Lett. 2015 Sep 14;589(19 Pt B):2675-82. doi: 10.1016/j.febslet.2015.08.019. , Epub 2015 Aug 28. PMID:26318717 doi:http://dx.doi.org/10.1016/j.febslet.2015.08.019