7ybd: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

The ~~entry 7ybd~~ is ~~ON HOLD until Paper~~ Publication

==Crystal structure of sliding DNA clamp of Clostridioides difficile==

== Structural highlights ==

<table><tr><td colspan='2'>[[7ybd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YBD FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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=7ybd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ybd OCA], [https://pdbe.org/7ybd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ybd RCSB], [https://www.ebi.ac.uk/pdbsum/7ybd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ybd ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q18C88_CLOD6 Q18C88_CLOD6] Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication.[ARBA:ARBA00002266][PIRNR:PIRNR000804]

== Publication Abstract from PubMed ==

The sliding DNA clamp is a ring-shaped protein that encircles DNA within its central channel. It binds to multiple proteins, such as DNA polymerases and DNA repair enzymes, and stimulates their enzymatic activities, thereby playing a crucial role in cell survival and proliferation. Accordingly, the bacterial clamp DnaN is considered to be a promising target for bacterial infection therapy. In this regard, three-dimensional structures of DnaN from pathogenic bacteria are essential for the development of chemical compounds with antimicrobial activity. Here, the crystal structure of DnaN from a Gram-positive bacterium Clostridioides difficile, a human pathogen causing infectious diarrhea, has been determined at 2.13 A resolution. Comparison of the structures of DnaN from other bacteria indicates that the structural features of DnaN in terms of overall organization are essentially conserved within Gram-positive and Gram-negative bacteria. However, DnaN from C. difficile has structural differences in the potential binding pocket for partner proteins, implying a non-conventional interaction with its binding partners. Our findings will provide insight into the development of new therapies for C. difficile infection.

~~Authors~~:

Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile.,Hishiki A, Okazaki S, Hara K, Hashimoto H J Biochem. 2022 Sep 27. pii: 6724376. doi: 10.1093/jb/mvac079. PMID:36166824<ref>PMID:36166824</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Clostridioides difficile]]

[[Category: Large Structures]]

[[Category: Hara K]]

[[Category: Hashimoto H]]

[[Category: Hishiki A]]

[[Category: Okazaki S]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7ybd is ON HOLD  until Paper Publication
+==Crystal structure of sliding DNA clamp of Clostridioides difficile==
+<StructureSection load='7ybd' size='340' side='right'caption='[[7ybd]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7ybd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YBD FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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=7ybd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ybd OCA], [https://pdbe.org/7ybd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ybd RCSB], [https://www.ebi.ac.uk/pdbsum/7ybd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ybd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q18C88_CLOD6 Q18C88_CLOD6] Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication.[ARBA:ARBA00002266][PIRNR:PIRNR000804]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The sliding DNA clamp is a ring-shaped protein that encircles DNA within its central channel. It binds to multiple proteins, such as DNA polymerases and DNA repair enzymes, and stimulates their enzymatic activities, thereby playing a crucial role in cell survival and proliferation. Accordingly, the bacterial clamp DnaN is considered to be a promising target for bacterial infection therapy. In this regard, three-dimensional structures of DnaN from pathogenic bacteria are essential for the development of chemical compounds with antimicrobial activity. Here, the crystal structure of DnaN from a Gram-positive bacterium Clostridioides difficile, a human pathogen causing infectious diarrhea, has been determined at 2.13 A resolution. Comparison of the structures of DnaN from other bacteria indicates that the structural features of DnaN in terms of overall organization are essentially conserved within Gram-positive and Gram-negative bacteria. However, DnaN from C. difficile has structural differences in the potential binding pocket for partner proteins, implying a non-conventional interaction with its binding partners. Our findings will provide insight into the development of new therapies for C. difficile infection.
-Authors:
+Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile.,Hishiki A, Okazaki S, Hara K, Hashimoto H J Biochem. 2022 Sep 27. pii: 6724376. doi: 10.1093/jb/mvac079. PMID:36166824<ref>PMID:36166824</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7ybd" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Clostridioides difficile]]
+[[Category: Large Structures]]
+[[Category: Hara K]]
+[[Category: Hashimoto H]]
+[[Category: Hishiki A]]
+[[Category: Okazaki S]]