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4trt

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Deinococcus radiodurans DNA polymerase III subunit beta

Structural highlights

4trt is a 2 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9RYE8_DEIRA 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.[PIRNR:PIRNR000804]

Publication Abstract from PubMed

BACKGROUND: Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III beta subunit (beta-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans beta-clamp (Drbeta-clamp) at 2.0 A resolution. RESULTS: The sequence verification process revealed that at the time of the study the gene encoding Drbeta-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial beta-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution. CONCLUSIONS: The structure of Drbeta-clamp was determined to 2.0 A resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation.

Crystal structure of the DNA polymerase III beta subunit (beta-clamp) from the extremophile Deinococcus radiodurans.,Niiranen L, Lian K, Johnson KA, Moe E BMC Struct Biol. 2015 Feb 27;15(1):5. doi: 10.1186/s12900-015-0032-6. PMID:25886944^[1]

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

References

↑ Niiranen L, Lian K, Johnson KA, Moe E. Crystal structure of the DNA polymerase III beta subunit (beta-clamp) from the extremophile Deinococcus radiodurans. BMC Struct Biol. 2015 Feb 27;15(1):5. doi: 10.1186/s12900-015-0032-6. PMID:25886944 doi:http://dx.doi.org/10.1186/s12900-015-0032-6

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/4trt"

@@ Line 1: / Line 1: @@
 ==Deinococcus radiodurans DNA polymerase III subunit beta==
-<StructureSection load='4trt' size='340' side='right' caption='[[4trt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='4trt' size='340' side='right'caption='[[4trt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4trt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TRT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4trt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TRT FirstGlance]. <br>
-</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>
+</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&#8491;</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=4trt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4trt OCA], [http://pdbe.org/4trt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4trt RCSB], [http://www.ebi.ac.uk/pdbsum/4trt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4trt 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=4trt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4trt OCA], [https://pdbe.org/4trt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4trt RCSB], [https://www.ebi.ac.uk/pdbsum/4trt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4trt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q9RYE8_DEIRA Q9RYE8_DEIRA]] 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.[PIRNR:PIRNR000804]
+[https://www.uniprot.org/uniprot/Q9RYE8_DEIRA Q9RYE8_DEIRA] 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.[PIRNR:PIRNR000804]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 4trt" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Deinococcus radiodurans R1]]
-[[Category: Johnson, K A]]
+[[Category: Large Structures]]
-[[Category: Lian, K]]
+[[Category: Johnson KA]]
-[[Category: Moe, E]]
+[[Category: Lian K]]
-[[Category: Niiranen, L]]
+[[Category: Moe E]]
-[[Category: Dna clamp]]
+[[Category: Niiranen L]]
-[[Category: Transferase]]

4trt

From Proteopedia

Current revision

Deinococcus radiodurans DNA polymerase III subunit beta

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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