2ddg: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2ddg.png|left|200px]]


<!--
==Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA==
The line below this paragraph, containing "STRUCTURE_2ddg", creates the "Structure Box" on the page.
<StructureSection load='2ddg' size='340' side='right'caption='[[2ddg]], [[Resolution|resolution]] 2.10&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'>[[2ddg]] 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=2DDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDG 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]] 2.1&#8491;</td></tr>
-->
<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=ACT:ACETATE+ION'>ACT</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_2ddg| PDB=2ddg |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ddg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddg OCA], [https://pdbe.org/2ddg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddg RCSB], [https://www.ebi.ac.uk/pdbsum/2ddg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddg ProSAT], [https://www.topsan.org/Proteins/RSGI/2ddg 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/dd/2ddg_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=2ddg ConSurf].
<div style="clear:both"></div>


===Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA===
==See Also==
 
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 
== References ==
<!--
<references/>
The line below this paragraph, {{ABSTRACT_PUBMED_17870091}}, adds the Publication Abstract to the page
__TOC__
(as it appears on PubMed at http://www.pubmed.gov), where 17870091 is the PubMed ID number.
</StructureSection>
-->
[[Category: Large Structures]]
{{ABSTRACT_PUBMED_17870091}}
[[Category: Thermus thermophilus HB8]]
 
[[Category: Hoseki J]]
==About this Structure==
[[Category: Kosaka H]]
2DDG 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=2DDG OCA].
[[Category: Kuramitsu S]]
 
[[Category: Masui R]]
==Reference==
[[Category: Nakagawa N]]
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: Protein complex]]
[[Category: Thermus thermophilus hb8]]
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
[[Category: Base excision repair]]
[[Category: Dna complex]]
[[Category: Hydrolase/dna complex]]
[[Category: Iron/sulfer 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 20:07:42 2009''

Latest revision as of 16:47, 13 March 2024

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

Structural highlights

2ddg 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 2.1Å
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

2ddg, resolution 2.10Å

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=2ddg&oldid=4088682"