PDBsum entry 4zby

Hydrolase

PDB id

4zby

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Contents

			Protein chain

					194 a.a.

			Ligands

					SF4


					URA


					MES

			Waters ×200

PDB id:

4zby

Links

Name:

Hydrolase

Title:

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

Structure:

Uracil-DNA glycosylase. Chain: a. Fragment: residues 1-194. Engineered: yes

Source:

Sulfolobus tokodaii str. 7. Organism_taxid: 273063. Strain: 7. Gene: stk_22380. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å

R-factor:

0.167

R-free:

0.207

Authors:

A.Kawai,S.Miyamoto

Key ref:

A.Kawai et al. (2015). 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. PubMed id: 26318717 DOI: 10.1016/j.febslet.2015.08.019

Date:

15-Apr-15

Release date:

09-Sep-15

PROCHECK

	Headers

	References

Protein chain

Q96YD0 (UDGA_SULTO) - Type-4 uracil-DNA glycosylase from Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)

Seq: Struc:					220 a.a. 194 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.2.2.27 - uracil-DNA glycosylase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

DOI no: 10.1016/j.febslet.2015.08.019	Febs Lett 589:2675-2682 (2015)
PubMed id: 26318717

Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding.
A.Kawai, S.Higuchi, M.Tsunoda, K.T.Nakamura, Y.Yamagata, S.Miyamoto.

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.