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.


4yor

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:03, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 1.52A resolution.==
==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 1.52A resolution.==
-
<StructureSection load='4yor' size='340' side='right' caption='[[4yor]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
+
<StructureSection load='4yor' size='340' side='right'caption='[[4yor]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4yor]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOR FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4yor]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YOR FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.52&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yot|4yot]], [[4you|4you]], [[4yov|4yov]], [[4yow|4yow]], [[4yox|4yox]], [[4yoy|4yoy]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4yor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yor OCA], [http://pdbe.org/4yor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yor RCSB], [http://www.ebi.ac.uk/pdbsum/4yor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yor ProSAT]</span></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=4yor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yor OCA], [https://pdbe.org/4yor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yor RCSB], [https://www.ebi.ac.uk/pdbsum/4yor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yor ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/A0A060P168_PYRHR A0A060P168_PYRHR]
-
Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3'-5' exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3'-OH recognition site approximately 9 A away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required.
+
-
Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.,Miyazono KI, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M Nucleic Acids Res. 2015 Jul 2. pii: gkv654. PMID:26138487<ref>PMID:26138487</ref>
+
==See Also==
-
 
+
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4yor" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Pyrococcus shinkaii]]
+
[[Category: Large Structures]]
-
[[Category: Miyazono, K]]
+
[[Category: Pyrococcus horikoshii]]
-
[[Category: Tanokura, M]]
+
[[Category: Miyazono K]]
-
[[Category: Tsutsumi, K]]
+
[[Category: Tanokura M]]
-
[[Category: Exonuclease]]
+
[[Category: Tsutsumi K]]
-
[[Category: Hydrolase]]
+

Current revision

Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 1.52A resolution.

PDB ID 4yor

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/4yor"
Personal tools