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.

6jir

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of C. crescentus beta sliding clamp with PEG bound to putative beta-motif tethering region

Structural highlights

6jir is a 2 chain structure with sequence from Caulobacter vibrioides CB15. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3B_CAUVC 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.[UniProtKB:P0A988]

Publication Abstract from PubMed

The eubacterial beta sliding clamp (DnaN) plays a crucial role in DNA metabolism through direct interactions with DNA, polymerases and a variety of protein factors. A canonical protein-DnaN interaction has been identified in Escherichia coli and some other species, during which protein partners are tethered into the conserved canonical hydrophobic crevice of DnaN via the consensus beta-binding motif. Caulobacter crescentus is an excellent research model for use in the investigation of DNA replication and cell cycle regulation due to its unique asymmetric cell division pattern with restricted replication initiation; however, little is known about the specific features of C. crescentus DnaN (CcDnaN). Here, we report a significant divergence in the association of CcDnaN with proteins based on docking analysis and crystal structures that show that the beta-binding motifs of its protein partners bind a novel pocket instead of the canonical site. Pull-down and isothermal titration calorimetry (ITC) results revealed that mutations within the novel pocket disrupt protein-CcDnaN interactions. It was also shown by replication and RIDA (regulatory inactivation of DnaA) assays that mediation of protein interaction by the novel pocket is closely related to the performance of CcDnaN during replication and the DnaN-mediated regulation process. Moreover, assessments of clamp competition showed that DNA does not compete with protein partners when binding to the novel pocket. Overall, our structural and biochemical analyses provide strong evidence that CcDnaN employs a noncanonical protein association pattern.

Caulobacter crescentus beta sliding clamp employs a noncanonical regulatory model of DNA replication.,Jiang X, Zhang L, An J, Wang M, Teng M, Guo Q, Li X FEBS J. 2019 Nov 14. doi: 10.1111/febs.15138. PMID:31725950^[1]

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

References

↑ Jiang X, Zhang L, An J, Wang M, Teng M, Guo Q, Li X. Caulobacter crescentus beta sliding clamp employs a noncanonical regulatory model of DNA replication. FEBS J. 2019 Nov 14. doi: 10.1111/febs.15138. PMID:31725950 doi:http://dx.doi.org/10.1111/febs.15138

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Caulobacter vibrioides CB15 | Large Structures | Jiang X | Li X | Teng M

@@ Line 3: / Line 3: @@
 <StructureSection load='6jir' size='340' side='right'caption='[[6jir]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jir]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JIR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JIR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jir]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JIR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.95&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUVC])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <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'>[http://proteopedia.org/fgij/fg.htm?mol=6jir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jir OCA], [http://pdbe.org/6jir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jir RCSB], [http://www.ebi.ac.uk/pdbsum/6jir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jir 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=6jir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jir OCA], [https://pdbe.org/6jir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jir RCSB], [https://www.ebi.ac.uk/pdbsum/6jir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jir ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPO3B_CAUVC DPO3B_CAUVC]] 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.[UniProtKB:P0A988]
+[https://www.uniprot.org/uniprot/DPO3B_CAUVC DPO3B_CAUVC] 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.[UniProtKB:P0A988]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6jir" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cauvc]]
+[[Category: Caulobacter vibrioides CB15]]
 [[Category: Large Structures]]
-[[Category: Jiang, X]]
+[[Category: Jiang X]]
-[[Category: Li, X]]
+[[Category: Li X]]
-[[Category: Teng, M]]
+[[Category: Teng M]]
-[[Category: Caulobacter crescentus]]
-[[Category: Homodimer]]
-[[Category: Peptide bound]]
-[[Category: Transferase]]

6jir

From Proteopedia

Current revision

Crystal structure of C. crescentus beta sliding clamp with PEG bound to putative beta-motif tethering region

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox