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1cyy

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Revision as of 10:44, 19 May 2021

CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM

Structural highlights

1cyy is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1cy0, 1cy1, 1cy2, 1cy4, 1cy7, 1cy6, 1cy8, 1cy9
Activity:	DNA topoisomerase, with EC number 5.99.1.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TOP1_ECOLI] Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodiester backbone. It has been proposed that both type IA and type II enzymes change conformation dramatically during the reaction cycle in order to accomplish these transformations. In the case of Escherichia coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The fragment is composed of two domains, and while the domains themselves remain largely unchanged, their relative arrangement can change dramatically.

Conformational changes in E. coli DNA topoisomerase I.,Feinberg H, Lima CD, Mondragon A Nat Struct Biol. 1999 Oct;6(10):918-22. PMID:10504724^[4]

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

References

↑ Chen SJ, Wang JC. Identification of active site residues in Escherichia coli DNA topoisomerase I. J Biol Chem. 1998 Mar 13;273(11):6050-6. PMID:9497321
↑ Zhu CX, Tse-Dinh YC. The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. J Biol Chem. 2000 Feb 25;275(8):5318-22. PMID:10681504
↑ Zhang Z, Cheng B, Tse-Dinh YC. Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I. Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6939-44. Epub 2011 Apr 11. PMID:21482796 doi:http://dx.doi.org/10.1073/pnas.1100300108
↑ Feinberg H, Lima CD, Mondragon A. Conformational changes in E. coli DNA topoisomerase I. Nat Struct Biol. 1999 Oct;6(10):918-22. PMID:10504724 doi:10.1038/13283

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1cyy"

@@ Line 3: / Line 3: @@
 <StructureSection load='1cyy' size='340' side='right'caption='[[1cyy]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1cyy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CYY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1cyy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CYY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1cy0|1cy0]], [[1cy1|1cy1]], [[1cy2|1cy2]], [[1cy4|1cy4]], [[1cy7|1cy7]], [[1cy6|1cy6]], [[1cy8|1cy8]], [[1cy9|1cy9]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cy0|1cy0]], [[1cy1|1cy1]], [[1cy2|1cy2]], [[1cy4|1cy4]], [[1cy7|1cy7]], [[1cy6|1cy6]], [[1cy8|1cy8]], [[1cy9|1cy9]]</div></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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </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=1cyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cyy OCA], [http://pdbe.org/1cyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cyy RCSB], [http://www.ebi.ac.uk/pdbsum/1cyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cyy ProSAT]</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=1cyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cyy OCA], [https://pdbe.org/1cyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cyy RCSB], [https://www.ebi.ac.uk/pdbsum/1cyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cyy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TOP1_ECOLI TOP1_ECOLI]] Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.<ref>PMID:9497321</ref> <ref>PMID:10681504</ref> <ref>PMID:21482796</ref>
+[[https://www.uniprot.org/uniprot/TOP1_ECOLI TOP1_ECOLI]] Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.<ref>PMID:9497321</ref> <ref>PMID:10681504</ref> <ref>PMID:21482796</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Topoisomerase|Topoisomerase]]
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 == References ==
 <references/>

1cyy

From Proteopedia

Revision as of 10:44, 19 May 2021

CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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