This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2d3y

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:46, 13 March 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2d3y.png|left|200px]]
 
-
<!--
+
==Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8==
-
The line below this paragraph, containing "STRUCTURE_2d3y", creates the "Structure Box" on the page.
+
<StructureSection load='2d3y' size='340' side='right'caption='[[2d3y]], [[Resolution|resolution]] 1.55&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'>[[2d3y]] is a 1 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=2D3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3Y 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]] 1.55&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-
{{STRUCTURE_2d3y| PDB=2d3y | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3y OCA], [https://pdbe.org/2d3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3y RCSB], [https://www.ebi.ac.uk/pdbsum/2d3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3y ProSAT], [https://www.topsan.org/Proteins/RSGI/2d3y 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/d3/2d3y_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=2d3y ConSurf].
 +
<div style="clear:both"></div>
-
===Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8===
+
==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: Kosaka H]]
-
==About this Structure==
+
[[Category: Kuramitsu S]]
-
2D3Y is a [[Single protein]] structure of sequence 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=2D3Y OCA].
+
[[Category: Masui R]]
-
 
+
[[Category: Nakagawa N]]
-
==Reference==
+
-
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: Single protein]]
+
-
[[Category: Thermus thermophilus hb8]]
+
-
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+
-
[[Category: Base excision repair]]
+
-
[[Category: Hydrolase]]
+
-
[[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 20:12:22 2009''
+

Current revision

Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8

PDB ID 2d3y

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2d3y"
Personal tools