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.

6p74

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

OLD nuclease from Thermus Scotoductus

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6p74"

Categories: Large Structures | Thermus scotoductus | Chappie JS | Schiltz CJ

@@ Line 3: / Line 3: @@
 <StructureSection load='6p74' size='340' side='right'caption='[[6p74]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51532 Atcc 51532]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P74 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6p74]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_scotoductus Thermus scotoductus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P74 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P74 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TSC_c04750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37636 ATCC 51532])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [http://pdbe.org/6p74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [http://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 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=6p74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p74 OCA], [https://pdbe.org/6p74 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p74 RCSB], [https://www.ebi.ac.uk/pdbsum/6p74 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p74 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/OLD_THESS OLD_THESS] An exodeoxyribonuclease that degrades linear or supercoiled dsDNA from 5'-3'. Nicks and linearizes circular DNA. Activity is not stimulated by ATP or AMP-PNP, although it has DNA-stimulated ATPase activity.<ref>PMID:32009148</ref>
-OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 A resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC-Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.
-The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases.,Schiltz CJ, Adams MC, Chappie JS Nucleic Acids Res. 2020 Feb 3. pii: 5721213. doi: 10.1093/nar/gkaa059. PMID:32009148<ref>PMID:32009148</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6p74" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 51532]]
 [[Category: Large Structures]]
-[[Category: Chappie, J S]]
+[[Category: Thermus scotoductus]]
-[[Category: Schiltz, C J]]
+[[Category: Chappie JS]]
-[[Category: Abc atpase]]
+[[Category: Schiltz CJ]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]

6p74

From Proteopedia

Current revision

OLD nuclease from Thermus Scotoductus

Structural highlights

Function

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox