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5h0j

From Proteopedia

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<StructureSection load='5h0j' size='340' side='right'caption='[[5h0j]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='5h0j' size='340' side='right'caption='[[5h0j]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5h0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedhd Pedhd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H0J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H0J FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5h0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedobacter_heparinus_DSM_2366 Pedobacter heparinus DSM 2366]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H0J FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h0k|5h0k]]</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.801&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5h0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h0j OCA], [http://pdbe.org/5h0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h0j RCSB], [http://www.ebi.ac.uk/pdbsum/5h0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h0j ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5h0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h0j OCA], [https://pdbe.org/5h0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h0j RCSB], [https://www.ebi.ac.uk/pdbsum/5h0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h0j ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/C6Y1J8_PEDHD C6Y1J8_PEDHD]
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Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named as Phe SMUG2), which display catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. Phylogenetic analyses show that SMUG2 enzymes are closely related to family 3 SMUG1s but belong to a distinct branch of the family. The high solution crystal structure of the apoenzyme reveals that the general fold of Phe SMUG2 resembles SMUG1s, yet with several distinct local structural differences. Mutational studies, coupled with structural modeling, identify several important amino acid residues for the glycosylase activity. Substitution of G65 with a tyrosine results in loss of all glycosylase activity. The crystal structure of the G65Y mutant suggests a potential misalignment at the active site due to the mutation. The relationship between the new subfamily and other families in UDG superfamily is discussed. This study provides new mechanistic insight into the molecular mechanism of the UDG superfamily.
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SMUG2 DNA Glycosylase from Pedobacter heparinus as a New Subfamily in UDG Superfamily.,Pang P, Yang Y, Li J, Wang Z, Cao W, Xie W Biochem J. 2017 Jan 3. pii: BCJ20160934. doi: 10.1042/BCJ20160934. PMID:28049757<ref>PMID:28049757</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5h0j" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Pedhd]]
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[[Category: Pedobacter heparinus DSM 2366]]
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[[Category: Cao, W]]
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[[Category: Cao W]]
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[[Category: Pang, P]]
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[[Category: Pang P]]
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[[Category: Xie, W]]
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[[Category: Xie W]]
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[[Category: Dna damage]]
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[[Category: Glycosylase]]
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[[Category: Lyase]]
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[[Category: Smug]]
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Current revision

The crystal structure of WT Pedobacter heparinus SMUG2

PDB ID 5h0j

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