3px7: Difference between revisions

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<StructureSection load='3px7' size='340' side='right'caption='[[3px7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='3px7' size='340' side='right'caption='[[3px7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3px7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecod1 Ecod1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3px7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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]] 2.3&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ecl|1ecl]], [[1cy0|1cy0]], [[1cy4|1cy4]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">415337, EcDH1_2375 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1])</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'>[https://proteopedia.org/fgij/fg.htm?mol=3px7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px7 OCA], [https://pdbe.org/3px7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px7 RCSB], [https://www.ebi.ac.uk/pdbsum/3px7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px7 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=3px7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px7 OCA], [https://pdbe.org/3px7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px7 RCSB], [https://www.ebi.ac.uk/pdbsum/3px7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/C9QXS7_ECOD1 C9QXS7_ECOD1]] 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.[HAMAP-Rule:MF_00952][SAAS:SAAS00003469]
[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>


==See Also==
==See Also==
*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA topoisomerase]]
[[Category: Escherichia coli DH1]]
[[Category: Ecod1]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cheng, B]]
[[Category: Cheng B]]
[[Category: Tse-dinh, Y C]]
[[Category: Tse-dinh YC]]
[[Category: Zhang, Z]]
[[Category: Zhang Z]]
[[Category: Isomerase]]
[[Category: Isomerase-dna complex]]
[[Category: Topoisomerase]]

Latest revision as of 16:34, 1 March 2024

Crystal Structure of covalent complex of topoisomerase 1A with substrateCrystal Structure of covalent complex of topoisomerase 1A with substrate

Structural highlights

3px7 is a 3 chain structure with sequence from Escherichia coli DH1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:,
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]

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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

3px7, resolution 2.30Å

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