2dem: Difference between revisions

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{{Seed}}
[[Image:2dem.png|left|200px]]


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==Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA==
The line below this paragraph, containing "STRUCTURE_2dem", creates the "Structure Box" on the page.
<StructureSection load='2dem' size='340' side='right'caption='[[2dem]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2dem]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEM FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
{{STRUCTURE_2dem|  PDB=2dem  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dem OCA], [https://pdbe.org/2dem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dem RCSB], [https://www.ebi.ac.uk/pdbsum/2dem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dem ProSAT], [https://www.topsan.org/Proteins/RSGI/2dem TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/UDGB_THET8 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).<ref>PMID:12000829</ref> <ref>PMID:17870091</ref> <ref>PMID:24838246</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2dem_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dem ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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 Uracil-DNA glycosylase in complex with AP:A containing DNA===
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<ref>PMID:17870091</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2dem" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17870091}}, adds the Publication Abstract to the page
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17870091 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17870091}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2DEM is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEM OCA].
[[Category: Synthetic construct]]
 
[[Category: Thermus thermophilus HB8]]
==Reference==
[[Category: Hoseki J]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/17870091 17870091]
[[Category: Kosaka H]]
[[Category: Protein complex]]
[[Category: Kuramitsu S]]
[[Category: Thermus thermophilus hb8]]
[[Category: Masui R]]
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
[[Category: Nakagawa N]]
[[Category: Base excision repair]]
[[Category: Hydrolase/dna complex]]
[[Category: Iron/sulfur cluster]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Thermophile]]
[[Category: Uracil-dna glycosylase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan  7 20:16:46 2009''

Latest revision as of 11:26, 25 October 2023

Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNACrystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA

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.
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

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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

2dem, resolution 1.95Å

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