6rks: Difference between revisions

Latest revision as of 13:12, 22 May 2024

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertionE. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion

6rks, resolution 4.00Å

Structural highlights

6rks is a 8 chain structure with sequence from Escherichia coli and Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 4Å
Ligands:
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GYRA_ECOLI DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.^[1] ^[2] ^[3]

Publication Abstract from PubMed

DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 A enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates.

Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.,Vanden Broeck A, Lotz C, Ortiz J, Lamour V Nat Commun. 2019 Oct 30;10(1):4935. doi: 10.1038/s41467-019-12914-y. PMID:31666516^[4]

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

References

↑ Hockings SC, Maxwell A. Identification of four GyrA residues involved in the DNA breakage-reunion reaction of DNA gyrase. J Mol Biol. 2002 Apr 26;318(2):351-9. PMID:12051842 doi:http://dx.doi.org/10.1016/S0022-2836(02)00048-7
↑ Sissi C, Chemello A, Vazquez E, Mitchenall LA, Maxwell A, Palumbo M. DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action. Biochemistry. 2008 Aug 19;47(33):8538-45. doi: 10.1021/bi800480j. Epub 2008 Jul, 22. PMID:18642932 doi:http://dx.doi.org/10.1021/bi800480j
↑ Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CE, Le TB, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A. A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase. Science. 2009 Dec 4;326(5958):1415-8. PMID:19965760 doi:326/5958/1415
↑ Vanden Broeck A, Lotz C, Ortiz J, Lamour V. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun. 2019 Oct 30;10(1):4935. doi: 10.1038/s41467-019-12914-y. PMID:31666516 doi:http://dx.doi.org/10.1038/s41467-019-12914-y

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OCA

[1] Hockings SC, Maxwell A. Identification of four GyrA residues involved in the DNA breakage-reunion reaction of DNA gyrase. J Mol Biol. 2002 Apr 26;318(2):351-9. PMID:12051842 doi:http://dx.doi.org/10.1016/S0022-2836(02)00048-7

[2] Sissi C, Chemello A, Vazquez E, Mitchenall LA, Maxwell A, Palumbo M. DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action. Biochemistry. 2008 Aug 19;47(33):8538-45. doi: 10.1021/bi800480j. Epub 2008 Jul, 22. PMID:18642932 doi:http://dx.doi.org/10.1021/bi800480j

[3] Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CE, Le TB, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A. A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase. Science. 2009 Dec 4;326(5958):1415-8. PMID:19965760 doi:326/5958/1415

[4] Vanden Broeck A, Lotz C, Ortiz J, Lamour V. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun. 2019 Oct 30;10(1):4935. doi: 10.1038/s41467-019-12914-y. PMID:31666516 doi:http://dx.doi.org/10.1038/s41467-019-12914-y

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion==
-<StructureSection load='6rks' size='340' side='right'caption='[[6rks]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
+<SX load='6rks' size='340' side='right' viewer='molstar' caption='[[6rks]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6rks]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_o157:h7_str._ss52 Escherichia coli o157:h7 str. ss52]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RKS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6rks]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RKS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JHN:(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione'>JHN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrA, hisW, nalA, parD, b2231, JW2225 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), gyrB, SS52_4995 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1330457 Escherichia coli O157:H7 str. SS52])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JHN:(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione'>JHN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isomerase Isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.6.2.3 5.6.2.3] </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=6rks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rks OCA], [https://pdbe.org/6rks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rks RCSB], [https://www.ebi.ac.uk/pdbsum/6rks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rks 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=6rks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rks OCA], [http://pdbe.org/6rks PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rks RCSB], [http://www.ebi.ac.uk/pdbsum/6rks PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rks ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GYRA_ECOLI GYRA_ECOLI]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051842</ref> <ref>PMID:18642932</ref> <ref>PMID:19965760</ref>
+[https://www.uniprot.org/uniprot/GYRA_ECOLI GYRA_ECOLI] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051842</ref> <ref>PMID:18642932</ref> <ref>PMID:19965760</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6rks" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Gyrase 3D Structures|Gyrase 3D Structures]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Ecoli]]
+[[Category: Escherichia coli]]
-[[Category: Escherichia coli o157:h7 str. ss52]]
+[[Category: Escherichia coli K-12]]
-[[Category: Isomerase]]
 [[Category: Large Structures]]
-[[Category: Broeck, A Vanden]]
+[[Category: Lamour V]]
-[[Category: Lamour, V]]
+[[Category: Vanden Broeck A]]
-[[Category: Complex]]
-[[Category: Dna binding protein]]
-[[Category: Dna gyrase]]
-[[Category: Inhibitor]]

6rks: Difference between revisions

Latest revision as of 13:12, 22 May 2024

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertionE. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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6rks: Difference between revisions

Latest revision as of 13:12, 22 May 2024

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertionE. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

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