5m1s

From Proteopedia

(Difference between revisions)

Revision as of 06:27, 24 October 2018

Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode

Structural highlights

5m1s is a 7 chain structure with sequence from [1] and Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	dnaE, polC, b0184, JW0179 (ECOLI), dnaN, b3701, JW3678 (ECOLI), dnaQ, mutD, b0215, JW0205 (ECOLI), holE, b1842, JW1831 (ECOLI)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[HOLE_ECOLI] 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 exact function of the theta subunit is unknown. [DPO3A_ECOLI] 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 alpha chain is the DNA polymerase. [DPO3E_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease. [DPO3B_ECOLI] 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.

Publication Abstract from PubMed

Faithful DNA replication is essential to all forms of life and depends on the action of 3'-5' exonucleases that remove misincorporated nucleotides from the newly synthesized strand. However, how the DNA is transferred from the polymerase to the exonuclease active site is not known. Here we present the cryo-EM structure of the editing mode of the catalytic core of the Escherichia coli replisome, revealing a dramatic distortion of the DNA whereby the polymerase thumb domain acts as a wedge that separates the two DNA strands. Importantly, NMR analysis of the DNA substrate shows that the presence of a mismatch increases the fraying of the DNA, thus enabling it to reach the exonuclease active site. Therefore the mismatch corrects itself, whereas the exonuclease subunit plays a passive role. Hence, our work provides unique insights into high-fidelity replication and establishes a new paradigm for the correction of misincorporated nucleotides.

Self-correcting mismatches during high-fidelity DNA replication.,Fernandez-Leiro R, Conrad J, Yang JC, Freund SM, Scheres SH, Lamers MH Nat Struct Mol Biol. 2017 Jan 9. doi: 10.1038/nsmb.3348. PMID:28067916^[1]

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

References

↑ Fernandez-Leiro R, Conrad J, Yang JC, Freund SM, Scheres SH, Lamers MH. Self-correcting mismatches during high-fidelity DNA replication. Nat Struct Mol Biol. 2017 Jan 9. doi: 10.1038/nsmb.3348. PMID:28067916 doi:http://dx.doi.org/10.1038/nsmb.3348

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/5m1s"

@@ Line 3: / Line 3: @@
 <StructureSection load='5m1s' size='340' side='right' caption='[[5m1s]], [[Resolution|resolution]] 6.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5m1s]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M1S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5m1s]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M1S 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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaE, polC, b0184, JW0179 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), dnaN, b3701, JW3678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), dnaQ, mutD, b0215, JW0205 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), holE, b1842, JW1831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5m1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1s OCA], [http://pdbe.org/5m1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1s RCSB], [http://www.ebi.ac.uk/pdbsum/5m1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1s ProSAT]</span></td></tr>
 </table>
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5m1s" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase|DNA polymerase]]
 == References ==
 <references/>
@@ Line 23: / Line 27: @@
 </StructureSection>
 [[Category: DNA-directed DNA polymerase]]
+[[Category: Ecoli]]
 [[Category: Conrad, J]]
 [[Category: Fernandez-Leiro, R]]

5m1s

From Proteopedia

Revision as of 06:27, 24 October 2018

Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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