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| | <StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UI1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UI1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ui0|1ui0]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tthudg ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [https://pdbe.org/1ui1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [https://pdbe.org/1ui1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/UDGA_THET8 UDGA_THET8] Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair as well as from single-stranded DNA (PubMed:12000829, PubMed:14556741). Specifically recognizes uracil that is flipped out from double-stranded DNA (PubMed:14556741).<ref>PMID:12000829</ref> <ref>PMID:14556741</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hoseki, J]] | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Inoue, Y]] | + | [[Category: Hoseki J]] |
| - | [[Category: Kuramitsu, S]] | + | [[Category: Inoue Y]] |
| - | [[Category: Masui, R]] | + | [[Category: Kuramitsu S]] |
| - | [[Category: Okamoto, A]] | + | [[Category: Masui R]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Okamoto A]] |
| - | [[Category: Shibata, T]] | + | [[Category: Shibata T]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Base excision repair]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Iron/sulfer cluster]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Thermophile]]
| + | |
| - | [[Category: Uracil-dna glycosylase]]
| + | |
| Structural highlights
Function
UDGA_THET8 Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair as well as from single-stranded DNA (PubMed:12000829, PubMed:14556741). Specifically recognizes uracil that is flipped out from double-stranded DNA (PubMed:14556741).[1] [2]
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; EC 3.2.2.-) removes uracil from DNA to initiate DNA base excision repair. Since hydrolytic deamination of cytosine to uracil is one of the most frequent DNA-damaging events in all cells, UDG is an essential enzyme for maintaining the integrity of genomic information. For the first time, we report the crystal structure of a family 4 UDG from Thermus thermophilus HB8 (TthUDG) complexed with uracil, solved at 1.5 angstroms resolution. As opposed to UDG enzymes in its other families, TthUDG possesses a [4Fe-4S] cluster. This iron-sulfur cluster, which is distant from the active site, interacts with loop structures and has been suggested to be unessential to the activity but necessary for stabilizing the loop structures. In addition to the iron-sulfur cluster, salt-bridges and ion pairs on the molecular surface and the presence of proline on loops and turns is thought to contribute to the enzyme's thermostability. Despite very low levels of sequence identity with Escherichia coli and human UDGs (family 1) and E.coli G:T/U mismatch-specific DNA glycosylase (MUG) (family 2), the topology and order of secondary structures of TthUDG are similar to those of these distant relatives. Furthermore, the coordinates of the core structure formed by beta-strands are almost the same. Positive charge is distributed over the active-site groove, where TthUDG would bind DNA strands, as do UDG enzymes in other families. TthUDG recognizes uracil specifically in the same manner as does human UDG (family 1), rather than guanine in the complementary strand DNA, as does E.coli MUG (family 2). These results suggest that the mechanism by which family 4 UDGs remove uracils from DNA is similar to that of family 1 enzymes.
Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8.,Hoseki J, Okamoto A, Masui R, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S J Mol Biol. 2003 Oct 24;333(3):515-26. PMID:14556741[3]
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
- ↑ Hoseki J, Okamoto A, Masui R, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S. Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8. J Mol Biol. 2003 Oct 24;333(3):515-26. PMID:14556741
- ↑ Hoseki J, Okamoto A, Masui R, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S. Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8. J Mol Biol. 2003 Oct 24;333(3):515-26. PMID:14556741
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