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| | <StructureSection load='5ztj' size='340' side='right'caption='[[5ztj]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='5ztj' size='340' side='right'caption='[[5ztj]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ztj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhi"_schroeter_1886 "bacillus typhi" schroeter 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZTJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ztj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhi Salmonella enterica subsp. enterica serovar Typhi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZTJ FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90370 "Bacillus typhi" Schroeter 1886])</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]] 2.4Å</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_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5ztj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztj OCA], [https://pdbe.org/5ztj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ztj RCSB], [https://www.ebi.ac.uk/pdbsum/5ztj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztj ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ztj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztj OCA], [http://pdbe.org/5ztj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ztj RCSB], [http://www.ebi.ac.uk/pdbsum/5ztj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A1U7FVV6_SALET A0A1U7FVV6_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_01897] | + | [https://www.uniprot.org/uniprot/A0A1U7FVV6_SALET A0A1U7FVV6_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_01897] |
| | <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: Bacillus typhi schroeter 1886]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ethayathulla, A S]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhi]] |
| - | [[Category: Gupta, D]] | + | [[Category: Ethayathulla AS]] |
| - | [[Category: Kaur, G]] | + | [[Category: Gupta D]] |
| - | [[Category: Kaur, P]] | + | [[Category: Kaur G]] |
| - | [[Category: Sachdeva, E]] | + | [[Category: Kaur P]] |
| - | [[Category: Sharma, S]] | + | [[Category: Sachdeva E]] |
| - | [[Category: Singh, T P]] | + | [[Category: Sharma S]] |
| - | [[Category: Tiwari, P]] | + | [[Category: Singh TP]] |
| - | [[Category: Beta propeller]]
| + | [[Category: Tiwari P]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Gyr-ctd]]
| + | |
| - | [[Category: Topoisomerase]]
| + | |
| Structural highlights
Function
A0A1U7FVV6_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_01897]
Publication Abstract from PubMed
The essentiality of DNA Gyrase in basic cellular processes in bacterial pathogens makes it an ideal drug target. Though the Gyrase has a conserved mechanism of action, the complete DNA wrapping and binding process is still unknown. In this study, we have identified six arginine residues R556, R612, R667, R716, R766, and R817 in the DNA GyraseA - C-terminal domain from Salmonella enterica serovar Typhi (StGyrA-CTD) to be essential for DNA wrapping and sliding by a sequence and structure analysis. Through site-directed mutagenesis and EMSA studies, we observed that the substitution of R667 (blade 3) and R716 (blade 4) in StGyrA-CTD led to loss of DNA binding. Whereas, upon mutation of residue R612 (blade2), R766 (blade5) and R817 (blade6) along with supporting residue R712 (blade 4) a decrease in binding affinity was seen. Our results indicate that R667 and R716 act as a pivot point in DNA wrapping and sliding during gyrase catalytic activity. In this study, we propose that the DNA wrapping mechanism commences with DNA binding at blade3 and blade4 followed by other blades to facilitate the DNA sliding during supercoiling activity. This study provides a better understanding of the DNA binding and wrapping mechanism of GyrA-CTD in DNA Gyrase.
The pivot point arginines identified in the beta-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit.,Sachdeva E, Kaur G, Tiwari P, Gupta D, Singh TP, Ethayathulla AS, Kaur P Sci Rep. 2020 May 8;10(1):7817. doi: 10.1038/s41598-020-64792-w. PMID:32385379[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sachdeva E, Kaur G, Tiwari P, Gupta D, Singh TP, Ethayathulla AS, Kaur P. The pivot point arginines identified in the beta-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit. Sci Rep. 2020 May 8;10(1):7817. doi: 10.1038/s41598-020-64792-w. PMID:32385379 doi:http://dx.doi.org/10.1038/s41598-020-64792-w
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