Structural highlights
2dem is a 3 chain structure with sequence from Thermus thermophilus HB8 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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| Method: | X-ray diffraction, Resolution 1.95Å |
| Ligands: | , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN |
Function
UDGB_THET8 DNA glycosylase with broad substrate specificity. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair (PubMed:12000829, PubMed:17870091, PubMed:24838246). Can also excise hypoxanthine from double-stranded DNA containing G/I, T/I, and A/I base pairs, xanthine from both double-stranded and single stranded DNA, thymine from G/T mismatched DNA, 5'-hydroxymethyluracil and 5'-fluorouracil (PubMed:17870091, PubMed:24838246).[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Uracil-DNA glycosylase (UDG) removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. Within the UDG superfamily, a fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1-4. We have determined the crystal structure of a novel family 5 UDG from Thermus thermophilus HB8 complexed with DNA containing an abasic site. The active-site structure suggests this enzyme uses both steric force and water activation for its excision reaction. A conserved asparagine residue acts as a ligand to the catalytic water molecule. The structure also implies that another water molecule acts as a barrier during substrate recognition. Based on no significant open-closed conformational change upon binding to DNA, we propose a "slide-in" mechanism for initial damage recognition.
Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.,Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21. PMID:17870091[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Starkuviene V, Fritz HJ. A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res. 2002 May 15;30(10):2097-102. PMID:12000829 doi:10.1093/nar/30.10.2097
- ↑ Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R. Crystal structure of family 5 uracil-DNA glycosylase bound to DNA. J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21. PMID:17870091 doi:10.1016/j.jmb.2007.08.022
- ↑ Xia B, Liu Y, Li W, Brice AR, Dominy BN, Cao W. Specificity and catalytic mechanism in family 5 uracil DNA glycosylase. J Biol Chem. 2014 Jun 27;289(26):18413-26. PMID:24838246 doi:10.1074/jbc.M114.567354
- ↑ Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R. Crystal structure of family 5 uracil-DNA glycosylase bound to DNA. J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21. PMID:17870091 doi:10.1016/j.jmb.2007.08.022
