2dp6: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="2dp6" size="350" color="white" frame="true" align="right" spinBox="true" caption="2dp6, resolution 1.80Å" /> '''Crystal structure of...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2dp6.gif|left|200px]]<br /><applet load="2dp6" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2dp6, resolution 1.80&Aring;" />
'''Crystal structure of uracil-DNA glycosylase in complex with AP:C containing DNA'''<br />


==About this Structure==
==Crystal structure of uracil-DNA glycosylase in complex with AP:C containing DNA==
2DP6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=SF4:'>SF4</scene>, <scene name='pdbligand=2HP:'>2HP</scene>, <scene name='pdbligand=GOL:'>GOL</scene> and <scene name='pdbligand=EOH:'>EOH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DP6 OCA].
<StructureSection load='2dp6' size='340' side='right'caption='[[2dp6]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
[[Category: Single protein]]
== Structural highlights ==
[[Category: Thermus thermophilus]]
<table><tr><td colspan='2'>[[2dp6]] is a 3 chain structure with sequence from [https://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=2DP6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DP6 FirstGlance]. <br>
[[Category: Hoseki, J.]]
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
[[Category: Kosaka, H.]]
<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>
[[Category: Kuramitsu, S.]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dp6 OCA], [https://pdbe.org/2dp6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dp6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dp6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dp6 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dp6 TOPSAN]</span></td></tr>
[[Category: Masui, R.]]
</table>
[[Category: Nakagawa, N.]]
== Function ==
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[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>
[[Category: 2HP]]
== Evolutionary Conservation ==
[[Category: EOH]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: GOL]]
Check<jmol>
[[Category: SF4]]
  <jmolCheckbox>
[[Category: base excision repair]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/2dp6_consurf.spt"</scriptWhenChecked>
[[Category: dna complex]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: iron/sulfer cluster]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: national project on protein structural and functional analyses]]
  </jmolCheckbox>
[[Category: nppsfa]]
</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=2dp6 ConSurf].
[[Category: riken structural genomics/proteomics initiative]]
<div style="clear:both"></div>
[[Category: rsgi]]
[[Category: structural genomics]]
[[Category: thermophile]]
[[Category: uracil-dna glycosylase]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:10:27 2008''
==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Hoseki J]]
[[Category: Kosaka H]]
[[Category: Kuramitsu S]]
[[Category: Masui R]]
[[Category: Nakagawa N]]

Latest revision as of 11:27, 25 October 2023

Crystal structure of uracil-DNA glycosylase in complex with AP:C containing DNACrystal structure of uracil-DNA glycosylase in complex with AP:C containing DNA

Structural highlights

2dp6 is a 3 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
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.

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

2dp6, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2dp6&oldid=3923992"