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4rki

From Proteopedia

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Crystal structure of sliding beta clamp from Helicobacter pylori

Structural highlights

4rki is a 1 chain structure with sequence from Helicobacter pylori 26695. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3B_HELPY DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity).

Publication Abstract from PubMed

Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2A structure of beta-clamp from H. pylori (Hpbeta-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial beta-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of beta-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of beta-clamp binding regions in them and validated by SPR studies. Hpbeta-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of beta-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with beta-clamp.

Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.,Pandey P, Tarique KF, Mazumder M, Rehman SA, Kumari N, Gourinath S Sci Rep. 2016 Aug 8;6:31181. doi: 10.1038/srep31181. PMID:27499105^[1]

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

References

↑ Pandey P, Tarique KF, Mazumder M, Rehman SA, Kumari N, Gourinath S. Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori. Sci Rep. 2016 Aug 8;6:31181. doi: 10.1038/srep31181. PMID:27499105 doi:http://dx.doi.org/10.1038/srep31181

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/4rki"

@@ Line 3: / Line 3: @@
 <StructureSection load='4rki' size='340' side='right'caption='[[4rki]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RKI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rki]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RKI FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaN, HP_0500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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]] 2.05&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=4rki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rki OCA], [https://pdbe.org/4rki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rki RCSB], [https://www.ebi.ac.uk/pdbsum/4rki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rki 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=4rki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rki OCA], [http://pdbe.org/4rki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rki RCSB], [http://www.ebi.ac.uk/pdbsum/4rki PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rki ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPO3B_HELPY DPO3B_HELPY]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity).
+[https://www.uniprot.org/uniprot/DPO3B_HELPY DPO3B_HELPY] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 20: @@
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Campylobacter pylori]]
+[[Category: Helicobacter pylori 26695]]
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Large Structures]]
-[[Category: Gourinath, S]]
+[[Category: Abdul Rehman SA]]
-[[Category: Rehman, S A.Abdul]]
+[[Category: Gourinath S]]
-[[Category: Satyawali, P]]
+[[Category: Satyawali P]]
-[[Category: Tarique, K F]]
+[[Category: Tarique KF]]
-[[Category: Processivity promoting factor]]
-[[Category: Transferase]]

4rki

From Proteopedia

Current revision

Crystal structure of sliding beta clamp from Helicobacter pylori

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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