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6rks

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Revision as of 00:21, 7 March 2020

E. 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 Ecoli and Escherichia coli o157:h7 str. ss52. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	gyrA, hisW, nalA, parD, b2231, JW2225 (ECOLI), gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 (Escherichia coli O157:H7 str. SS52)
Activity:	DNA topoisomerase, with EC number 5.6.2.2
Experimental data:	Check to display Experimental Data
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] [GYRB_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.^[4] ^[5] ^[6]

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^[7]

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
↑ Noble CG, Maxwell A. The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J Mol Biol. 2002 Apr 26;318(2):361-71. PMID:12051843 doi:http://dx.doi.org/10.1016/S0022-2836(02)00049-9
↑ 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
↑ Schoeffler AJ, May AP, Berger JM. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res. 2010 Jul 31. PMID:20675723 doi:10.1093/nar/gkq665
↑ 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 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/6rks"

@@ 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>
@@ Line 20: / Line 20: @@
 </div>
 <div class="pdbe-citations 6rks" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: DNA topoisomerase]]
 [[Category: Ecoli]]

6rks

From Proteopedia

Revision as of 00:21, 7 March 2020

E. 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

Proteopedia Page Contributors and Editors (what is this?)

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