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| | <StructureSection load='6pcm' size='340' side='right'caption='[[6pcm]], [[Resolution|resolution]] 3.11Å' scene=''> | | <StructureSection load='6pcm' size='340' side='right'caption='[[6pcm]], [[Resolution|resolution]] 3.11Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6pcm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PCM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pcm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis] and [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PCM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 3.107Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">topA, MSMEG_6157, MSMEI_5999 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[http://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [http://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=6pcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcm OCA], [https://pdbe.org/6pcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pcm RCSB], [https://www.ebi.ac.uk/pdbsum/6pcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcm 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=6pcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pcm OCA], [http://pdbe.org/6pcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pcm RCSB], [http://www.ebi.ac.uk/pdbsum/6pcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pcm ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TOP1_MYCS2 TOP1_MYCS2]] 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 (PubMed:9593741) 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 (By similarity).[HAMAP-Rule:MF_00952]<ref>PMID:9593741</ref> Relaxes negatively (but not positively) supercoiled DNA, concatanates and knots circular ssDNA at 52 but not 37 degrees Celsius (PubMed:9593741). Preferentially nicks supercoiled DNA at C(G/T)CTT, cutting between the TT residues, binds ss and dsDNA with the recognition site (PubMed:10734203).<ref>PMID:10734203</ref> <ref>PMID:9593741</ref> | + | [https://www.uniprot.org/uniprot/TOP1_MYCS2 TOP1_MYCS2] 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 (PubMed:9593741) 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 (By similarity).[HAMAP-Rule:MF_00952]<ref>PMID:9593741</ref> Relaxes negatively (but not positively) supercoiled DNA, concatanates and knots circular ssDNA at 52 but not 37 degrees Celsius (PubMed:9593741). Preferentially nicks supercoiled DNA at C(G/T)CTT, cutting between the TT residues, binds ss and dsDNA with the recognition site (PubMed:10734203).<ref>PMID:10734203</ref> <ref>PMID:9593741</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6pcm" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6pcm" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Topoisomerase 3D structures|Topoisomerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA topoisomerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Mycs2]] | + | [[Category: Mycolicibacterium smegmatis]] |
| - | [[Category: Cao, N]] | + | [[Category: Mycolicibacterium smegmatis MC2 155]] |
| - | [[Category: Tan, K]] | + | [[Category: Cao N]] |
| - | [[Category: Tse-Dinh, Y C]] | + | [[Category: Tan K]] |
| - | [[Category: C-terminal domain]] | + | [[Category: Tse-Dinh YC]] |
| - | [[Category: Isomerase-dna complex]]
| + | |
| - | [[Category: N-terminal domain]]
| + | |
| - | [[Category: Ss dna binding]]
| + | |
| - | [[Category: Topoisomerase i]]
| + | |
| Structural highlights
Function
TOP1_MYCS2 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 (PubMed:9593741) 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 (By similarity).[HAMAP-Rule:MF_00952][1] Relaxes negatively (but not positively) supercoiled DNA, concatanates and knots circular ssDNA at 52 but not 37 degrees Celsius (PubMed:9593741). Preferentially nicks supercoiled DNA at C(G/T)CTT, cutting between the TT residues, binds ss and dsDNA with the recognition site (PubMed:10734203).[2] [3]
Publication Abstract from PubMed
Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.
Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains.,Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC Nucleic Acids Res. 2020 Mar 30. pii: 5813806. doi: 10.1093/nar/gkaa201. PMID:32232337[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bhaduri T, Bagui TK, Sikder D, Nagaraja V. DNA topoisomerase I from Mycobacterium smegmatis. An enzyme with distinct features. J Biol Chem. 1998 May 29;273(22):13925-32. doi: 10.1074/jbc.273.22.13925. PMID:9593741 doi:http://dx.doi.org/10.1074/jbc.273.22.13925
- ↑ Sikder D, Nagaraja V. Determination of the recognition sequence of Mycobacterium smegmatis topoisomerase I on mycobacterial genomic sequences. Nucleic Acids Res. 2000 Apr 15;28(8):1830-7. doi: 10.1093/nar/28.8.1830. PMID:10734203 doi:http://dx.doi.org/10.1093/nar/28.8.1830
- ↑ Bhaduri T, Bagui TK, Sikder D, Nagaraja V. DNA topoisomerase I from Mycobacterium smegmatis. An enzyme with distinct features. J Biol Chem. 1998 May 29;273(22):13925-32. doi: 10.1074/jbc.273.22.13925. PMID:9593741 doi:http://dx.doi.org/10.1074/jbc.273.22.13925
- ↑ Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC. Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains. Nucleic Acids Res. 2020 Mar 30. pii: 5813806. doi: 10.1093/nar/gkaa201. PMID:32232337 doi:http://dx.doi.org/10.1093/nar/gkaa201
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