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.


3ayv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:02, 13 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==TTHB071 protein from Thermus thermophilus HB8 soaking with ZnCl2==
==TTHB071 protein from Thermus thermophilus HB8 soaking with ZnCl2==
-
<StructureSection load='3ayv' size='340' side='right' caption='[[3ayv]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+
<StructureSection load='3ayv' size='340' side='right'caption='[[3ayv]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ayv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AYV FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ayv]] is a 4 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=3AYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AYV FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ayt|3ayt]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHB071 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ayv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ayv OCA], [https://pdbe.org/3ayv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ayv RCSB], [https://www.ebi.ac.uk/pdbsum/3ayv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ayv ProSAT]</span></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ayv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ayv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ayv RCSB], [http://www.ebi.ac.uk/pdbsum/3ayv PDBsum]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q53W91_THET8 Q53W91_THET8]
-
Accumulating genome sequences have revealed the existence of a large number of conserved hypothetical proteins. Characterization of these proteins is considered essential in the elucidation of intracellular biological pathways. Our previous transcriptomic analysis suggested that, in Thermus thermophilus HB8, loss of an oxidized DNA-repairing activity leads to the up-regulation of a function-unknown gene, tthb071, which is conserved in a wide range of bacteria. Interestingly, the tthb071 gene product, TTHB071, showed a significant primary structure similarity to apurinic/apyrimidinic (AP) endonucleases, which are required for the repair of oxidized DNA. In the present study, we observed that disruption of tthb071 increases the H(2)O(2) sensitivity in T. thermophilus HB8, suggesting the involvement of tthb071 in a protection mechanism against oxidative stress. However, purified TTHB071 exhibited no AP endonuclease or DNA-binding activities, indicating that TTHB071 plays no major role in repairing oxidative DNA damage. Then we determined the three-dimensional structure of TTHB071 complexed with zinc ions by x-ray crystallography. In addition to the overall structural similarity, the zinc-binding fashion was almost identical to that of the phosphatase active site of an AP endonuclease, implying that TTHB071 possesses a phosphatase activity. Based on the structural information around the zinc-binding site, we investigated the binding of TTHB071 to 14 different compounds. As a result, TTHB071 favorably bound FMN and pyridoxal phosphate in a zinc ion-mediated manner. Our results suggest that TTHB071 protects the cell from oxidative stress, through controlling the metabolism of FMN, pyridoxal phosphate, or an analogous compound.
+
-
 
+
-
In vivo, in vitro, and x-ray crystallographic analyses suggest the involvement of an uncharacterized triose-phosphate isomerase (TIM) barrel protein in protection against oxidative stress.,Nakane S, Wakamatsu T, Masui R, Kuramitsu S, Fukui K J Biol Chem. 2011 Dec 2;286(48):41636-46. Epub 2011 Oct 7. PMID:21984829<ref>PMID:21984829</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Thet8]]
+
[[Category: Large Structures]]
-
[[Category: Fukui, K]]
+
[[Category: Thermus thermophilus HB8]]
-
[[Category: Kuramitsu, S]]
+
[[Category: Fukui K]]
-
[[Category: Masui, R]]
+
[[Category: Kuramitsu S]]
-
[[Category: Nakagawa, N]]
+
[[Category: Masui R]]
-
[[Category: Nakane, S]]
+
[[Category: Nakagawa N]]
-
[[Category: Structural genomic]]
+
[[Category: Nakane S]]
-
[[Category: Wakamatsu, T]]
+
[[Category: Wakamatsu T]]
-
[[Category: Rsgi]]
+
-
[[Category: Tim barrel]]
+
-
[[Category: Unknown function]]
+

Current revision

TTHB071 protein from Thermus thermophilus HB8 soaking with ZnCl2

PDB ID 3ayv

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/3ayv"
Personal tools