4juo: Difference between revisions

Revision as of 11:26, 30 November 2022

A low-resolution three-gate structure of topoisomerase IV from Streptococcus pneumoniae in space group H32

Structural highlights

4juo is a 6 chain structure with sequence from Streptococcus pneumoniae TIGR4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	LFX, MG
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 regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important beta-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 A, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.

Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.,Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR Nucleic Acids Res. 2013 Aug 21. PMID:23965305^[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, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport. Nucleic Acids Res. 2013 Aug 21. PMID:23965305 doi:10.1093/nar/gkt749

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, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport. Nucleic Acids Res. 2013 Aug 21. PMID:23965305 doi:10.1093/nar/gkt749

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==A low-resolution three-gate structure of topoisomerase IV from Streptococcus pneumoniae in space group H32==
-<StructureSection load='4juo' size='340' side='right' caption='[[4juo]], [[Resolution|resolution]] 6.53&Aring;' scene=''>
+<StructureSection load='4juo' size='340' side='right'caption='[[4juo]], [[Resolution|resolution]] 6.53&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4juo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JUO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JUO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4juo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JUO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LFX:(3S)-9-FLUORO-3-METHYL-10-(4-METHYLPIPERAZIN-1-YL)-7-OXO-2,3-DIHYDRO-7H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6-CARBOXYLIC+ACID'>LFX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LFX:(3S)-9-FLUORO-3-METHYL-10-(4-METHYLPIPERAZIN-1-YL)-7-OXO-2,3-DIHYDRO-7H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6-CARBOXYLIC+ACID'>LFX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4i3h|4i3h]], [[3rad|3rad]], [[3rae|3rae]], [[3raf|3raf]], [[3ksa|3ksa]], [[3ksb|3ksb]], [[3ltn|3ltn]], [[3k9f|3k9f]], [[3foe|3foe]], [[3fof|3fof]], [[2nov|2nov]]</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=4juo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4juo OCA], [https://pdbe.org/4juo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4juo RCSB], [https://www.ebi.ac.uk/pdbsum/4juo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4juo ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">parC, SP_0855 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN]), parE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4juo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4juo OCA], [http://pdbe.org/4juo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4juo RCSB], [http://www.ebi.ac.uk/pdbsum/4juo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4juo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PARC_STRPN PARC_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>  [[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 21: / Line 18: @@
 </div>
 <div class="pdbe-citations 4juo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Strpn]]
+[[Category: Large Structures]]
-[[Category: Crevel, I]]
+[[Category: Streptococcus pneumoniae TIGR4]]
-[[Category: Fisher, L M]]
+[[Category: Crevel I]]
-[[Category: Laponogov, I]]
+[[Category: Fisher LM]]
-[[Category: Pan, X S]]
+[[Category: Laponogov I]]
-[[Category: Sanderson, M R]]
+[[Category: Pan X-S]]
-[[Category: Veselkov, D A]]
+[[Category: Sanderson MR]]
-[[Category: Atp binding]]
+[[Category: Veselkov DA]]
-[[Category: Full-length pare]]
-[[Category: Isomerase-dna complex]]
-[[Category: Open n-gate]]
-[[Category: Parc55]]
-[[Category: Topoisomerase iia]]

4juo: Difference between revisions

Revision as of 11:26, 30 November 2022

A low-resolution three-gate structure of topoisomerase IV from Streptococcus pneumoniae in space group H32

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools