3rb9: Difference between revisions

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<StructureSection load='3rb9' size='340' side='right'caption='[[3rb9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='3rb9' size='340' side='right'caption='[[3rb9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rb9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RB9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rb9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RB9 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaN, MT0002, MTCY10H4.0, MTV029.02, Rv0002 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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]] 3&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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=3rb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rb9 OCA], [https://pdbe.org/3rb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rb9 RCSB], [https://www.ebi.ac.uk/pdbsum/3rb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rb9 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=3rb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rb9 OCA], [https://pdbe.org/3rb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rb9 RCSB], [https://www.ebi.ac.uk/pdbsum/3rb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rb9 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DPO3B_MYCTU DPO3B_MYCTU]] 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_MYCTU DPO3B_MYCTU] 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 ==
The sliding beta-clamp, an important component of the DNA replication and repair machinery, is drawing increasing attention as a therapeutic target. We report the crystal structure of the M. tuberculosis beta-clamp (Mtbbeta-clamp) to 3.0 A resolution. The protein crystallized in the space group C222(1) with cell-dimensions a = 72.7, b = 234.9 &amp; c = 125.1 A respectively. Mtbbeta-clamp is a dimer, and exhibits head-to-tail association similar to other bacterial clamps. Each monomer folds into three domains with similar structures respectively and associates with its dimeric partner through 6 salt-bridges and about 21 polar interactions. Affinity experiments involving a blunt DNA duplex, primed-DNA and nicked DNA respectively show that Mtbbeta-clamp binds specifically to primed DNA about 1.8 times stronger compared to the other two substrates and with an apparent K(d) of 300 nM. In bacteria like E. coli, the beta-clamp is known to interact with subunits of the clamp loader, NAD(+)-dependent DNA ligase (LigA) and other partners. We tested the interactions of the Mtbbeta-clamp with MtbLigA and the gamma-clamp loader subunit through radioactive gel shift assays, size exclusion chromatography, yeast-two hybrid experiments and also functionally. Intriguingly while Mtbbeta-clamp interacts in vitro with the gamma-clamp loader, it does not interact with MtbLigA unlike in bacteria like E. coli where it does. Modeling studies involving earlier peptide complexes reveal that the peptide-binding site is largely conserved despite lower sequence identity between bacterial clamps. Overall the results suggest that other as-yet-unidentified factors may mediate interactions between the clamp, LigA and DNA in mycobacteria.


M. tuberculosis sliding beta-clamp does not interact directly with the NAD+-dependent DNA ligase.,Kukshal V, Khanam T, Chopra D, Singh N, Sanyal S, Ramachandran R PLoS One. 2012;7(4):e35702. Epub 2012 Apr 24. PMID:22545130<ref>PMID:22545130</ref>
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3rb9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Myctu]]
[[Category: Mycobacterium tuberculosis H37Rv]]
[[Category: Kukshal, V]]
[[Category: Kukshal V]]
[[Category: Ramachandran, R]]
[[Category: Ramachandran R]]
[[Category: Beta clamp]]
[[Category: Clamp loader]]
[[Category: Dna sliding beta clamp]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Transferase]]

Latest revision as of 11:35, 20 March 2024

Crystal structure of the M. tuberculosis beta clampCrystal structure of the M. tuberculosis beta clamp

Structural highlights

3rb9 is a 2 chain structure with sequence from Mycobacterium tuberculosis H37Rv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3B_MYCTU 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).

See Also

3rb9, resolution 3.00Å

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OCA
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