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| | <StructureSection load='5zxm' size='340' side='right'caption='[[5zxm]], [[Resolution|resolution]] 1.94Å' scene=''> | | <StructureSection load='5zxm' size='340' side='right'caption='[[5zxm]], [[Resolution|resolution]] 1.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salet Salet]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZXM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica Salmonella enterica subsp. enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZXM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.938Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=59201 SALET])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5.6.2.2 5.6.2.2] </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=5zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxm OCA], [https://pdbe.org/5zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zxm RCSB], [https://www.ebi.ac.uk/pdbsum/5zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxm 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=5zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxm OCA], [https://pdbe.org/5zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zxm RCSB], [https://www.ebi.ac.uk/pdbsum/5zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/A0A3R0U328_SALET A0A3R0U328_SALET]] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01898]
| + | [https://www.uniprot.org/uniprot/A0A3R0U328_SALET A0A3R0U328_SALET] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01898] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA topoisomerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Salet]] | + | [[Category: Salmonella enterica subsp. enterica]] |
| - | [[Category: Ethayathulla, A S]] | + | [[Category: Ethayathulla AS]] |
| - | [[Category: Gupta, D]] | + | [[Category: Gupta D]] |
| - | [[Category: Kaur, P]] | + | [[Category: Kaur P]] |
| - | [[Category: Sachdeva, E]] | + | [[Category: Sachdeva E]] |
| - | [[Category: Sharma, S]] | + | [[Category: Sharma S]] |
| - | [[Category: Singh, T P]] | + | [[Category: Singh TP]] |
| - | [[Category: Tiwari, P]] | + | [[Category: Tiwari P]] |
| - | [[Category: Atp binding domain]]
| + | |
| - | [[Category: Gyrb-ntd]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Topoisomerase]]
| + | |
| Structural highlights
5zxm is a 2 chain structure with sequence from Salmonella enterica subsp. enterica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.938Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A3R0U328_SALET A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01898]
Publication Abstract from PubMed
DNA Gyrase is a type II topoisomerase that utilizes the energy of ATP hydrolysis for introducing negative supercoils in DNA. The protein comprises two subunits GyrA and GyrB that form a GyrA2GyrB2 heterotetramer. GyrB subunit contains the N-terminal domain (GBNTD) for ATPase activity and the C-terminal domain (GBCTD) for interaction with GyrA and DNA. Earlier structural studies have revealed three different conformational states for GBNTD during ATP hydrolysis defined as open, semi-open, and closed. Here we report, the three-dimensional structure of a new transient closed conformation of GBNTD from Salmonella Typhi (StGBNTD) at 1.94 A resolution. Based on the structural analysis of this transient closed conformation, we propose the role of protein in the mechanism of ATP hydrolysis. We further explored the effect of pH on ATPase activity and structural stability of the GBNTD using CD and fluorescence spectroscopy at varying pH environment. Kinetic parameters obtained from the ATPase assay were correlated with its secondary and tertiary structure at their respective pH environment. The protein possessed maximum ATPase activity and structural stability at optimum pH 8. At acidic pH, a remarkable decrease in both enzymatic activity and structural stability was observed whereas at alkaline pH there was no significant change. The structural analysis of StGBNTD reveals the role of polar interactions in stabilizing the overall dimeric conformation of the protein.
Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain.,Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P Arch Biochem Biophys. 2021 Feb 3;701:108786. doi: 10.1016/j.abb.2021.108786. PMID:33548211[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P. Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain. Arch Biochem Biophys. 2021 Feb 3;701:108786. doi: 10.1016/j.abb.2021.108786. PMID:33548211 doi:http://dx.doi.org/10.1016/j.abb.2021.108786
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