5j5p: Difference between revisions

Latest revision as of 10:49, 6 September 2023

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I

Structural highlights

5j5p is a 6 chain structure with sequence from Streptococcus pneumoniae and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.97Å
Ligands:	ANP, MG, NA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PARE_STRPN Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.^[1] ^[2]

Publication Abstract from PubMed

Type II topoisomerases alter DNA topology to control DNA supercoiling and chromosome segregation and are targets of clinically important anti-infective and anticancer therapeutics. They act as ATP-operated clamps to trap a DNA helix and transport it through a transient break in a second DNA. Here, we present the first X-ray crystal structure solved at 2.83 A of a closed clamp complete with trapped T-segment DNA obtained by co-crystallizing the ATPase domain of S. pneumoniae topoisomerase IV with a nonhydrolyzable ATP analogue and 14-mer duplex DNA. The ATPase dimer forms a 22 A protein hole occupied by the kinked DNA bound asymmetrically through positively charged residues lining the hole, and whose mutagenesis impacts the DNA decatenation, DNA relaxation and DNA-dependent ATPase activities of topo IV. These results and a side-bound DNA-ParE structure help explain how the T-segment DNA is captured and transported by a type II topoisomerase, and reveal a new enzyme-DNA interface for drug discovery.

Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase.,Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR Nat Commun. 2018 Jul 3;9(1):2579. doi: 10.1038/s41467-018-05005-x. PMID:29968711^[3]

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

References

↑ Laponogov I, Veselkov DA, Sohi MK, Pan XS, Achari A, Yang C, Ferrara JD, Fisher LM, Sanderson MR. Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target. PLoS ONE. 2007 Mar 21;2(3):e301. PMID:17375187 doi:10.1371/journal.pone.0000301
↑ Laponogov I, Pan XS, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR. Structural basis of gate-DNA breakage and resealing by type II topoisomerases. PLoS One. 2010 Jun 28;5(6):e11338. PMID:20596531 doi:10.1371/journal.pone.0011338
↑ Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR. Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase. Nat Commun. 2018 Jul 3;9(1):2579. doi: 10.1038/s41467-018-05005-x. PMID:29968711 doi:https://dx.doi.org/10.1038/s41467-018-05005-x

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Laponogov I, Veselkov DA, Sohi MK, Pan XS, Achari A, Yang C, Ferrara JD, Fisher LM, Sanderson MR. Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target. PLoS ONE. 2007 Mar 21;2(3):e301. PMID:17375187 doi:10.1371/journal.pone.0000301

[2] Laponogov I, Pan XS, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR. Structural basis of gate-DNA breakage and resealing by type II topoisomerases. PLoS One. 2010 Jun 28;5(6):e11338. PMID:20596531 doi:10.1371/journal.pone.0011338

[3] Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR. Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase. Nat Commun. 2018 Jul 3;9(1):2579. doi: 10.1038/s41467-018-05005-x. PMID:29968711 doi:https://dx.doi.org/10.1038/s41467-018-05005-x

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I==
-<StructureSection load='5j5p' size='340' side='right' caption='[[5j5p]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+<StructureSection load='5j5p' size='340' side='right'caption='[[5j5p]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5j5p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J5P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5j5p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J5P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.97&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">parE, SP_0852 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5j5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5p OCA], [https://pdbe.org/5j5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j5p RCSB], [https://www.ebi.ac.uk/pdbsum/5j5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5p 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=5j5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5p OCA], [http://pdbe.org/5j5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j5p RCSB], [http://www.ebi.ac.uk/pdbsum/5j5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5p ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN]] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>
+[https://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Topoisomerase|Topoisomerase]]
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Fisher, L M]]
+[[Category: Large Structures]]
-[[Category: Laponogov, I]]
-[[Category: Pan, X S]]
-[[Category: Sanderson, M R]]
-[[Category: Skamrova, G]]
-[[Category: Umrekar, T]]
-[[Category: Atpase domain]]
-[[Category: Dna binding]]
-[[Category: Isomerase]]
-[[Category: Isomerase-dna complex]]
 [[Category: Streptococcus pneumoniae]]
-[[Category: T-segment]]
+[[Category: Synthetic construct]]
-[[Category: Topoisomerase iv]]
+[[Category: Fisher LM]]
+[[Category: Laponogov I]]
+[[Category: Pan X-S]]
+[[Category: Sanderson MR]]
+[[Category: Skamrova G]]
+[[Category: Umrekar T]]

5j5p: Difference between revisions

Latest revision as of 10:49, 6 September 2023

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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