User:Isabelle Kressy/Sandbox 1
From Proteopedia
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== Structural Description == | == Structural Description == | ||
- | The active site is a tetramer made up of <scene name='90/909964/Parc/3'>ParC</scene> and <scene name='90/909964/Pare/3'>ParE</scene> subunits. The ParC subunit contains an N-terminal DNA breakage-reunion domain, which is linked to C-terminal β-pinwheel | + | The active site is a tetramer made up of <scene name='90/909964/Parc/3'>ParC</scene> and <scene name='90/909964/Pare/3'>ParE</scene> subunits. The ParC subunit contains an N-terminal DNA breakage-reunion domain, which is linked to the C-terminal domain (CTD) that forms a β-pinwheel shape and functions for DNA binding. This favors the passage of DNA and DNA unlinking from the complex. In contrast, the N-terminal of the ParE subunits forms the ATPase domain. Additionally, ParE has a C-terminal Mg2+ binding domain. The C-gate consists of the two ParC subunits and the G-gate consists of the two ParE subunits. |
== Structure Insights == | == Structure Insights == |
Revision as of 03:27, 3 May 2022
Contents |
Quinolone(Clinafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae
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Topoisomerase IV in S. pneumoniae is a paralogue of type II topoisomerase. This structure is a complex of topoisomerase, DNA, and Quinolone, a drug that targets type II topoisomerases in Gram-negative and Gram-positive bacteria [1]. Topoisomerase IV consists of two subunits that function to regulate supercoiling and disentangle DNA.
Function
The main function of topoisomerase IV is to regulate the level of DNA supercoiling within the cell so that replication, transcription, and repair can take place [2].
In general, type II topoisomerases undergo a strand-passage mechanism to remove supercoiling and disentangle chromosomes. These enzymes cleave both strands of DNA and then pass a second duplex through the break using ATP. The cleaved strands are ligated together again and the two products are released from the enzyme [3].
Structural Description
The active site is a tetramer made up of and subunits. The ParC subunit contains an N-terminal DNA breakage-reunion domain, which is linked to the C-terminal domain (CTD) that forms a β-pinwheel shape and functions for DNA binding. This favors the passage of DNA and DNA unlinking from the complex. In contrast, the N-terminal of the ParE subunits forms the ATPase domain. Additionally, ParE has a C-terminal Mg2+ binding domain. The C-gate consists of the two ParC subunits and the G-gate consists of the two ParE subunits.
Structure Insights
Upon binding the ATPase domains, the G-segment distorts from linear B form to bent and extended A form DNA. The T-segment approaches and is “captured” by the ATPase domains. When the T-segment is “captured”, it moves to the middle of the two ATPase domains. Topo IV intercalates the T-segment into its major groove to provide binding stability. Once the two DNA duplexes are in place, the ATPase domains use ATP to cause cross interpolation of the first 20 residues of ParE and dimerizing the two ATPase domains. This causes DNA cleavage in the G-segment by both ParC and ParE. Active-site tyrosines (Y118 on ParC) bind to 5’ phosphates on the G-segment to cause a double-stranded break. This, paired with the torsional stress on the G-segment, mediate the cleavage. When the DNA-gate opens to let the T-segment through, the ATPase domains rotate the T-segment by 45˚ and simultaneously moves alpha helices from the ParE subunits out of the way for the T-segment to pass. Once the T-segment is next to the C-gate, the G-gate closes and reseals the G-segment, which causes T-segment release by the opening and closing of the C-gate. Closure of the G-gate is caused by the ATPase domains rotating to its original position, inducing ATP hydrolysis, and releasing ADP and the G-segment.
Evolutionarily Related Proteins
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Topo IV works closely with gyrase, another type II topoisomerase, to uncoil DNA and ensure that replication can take place. Its main function is to relax positive supercoils and catalyze the formation of negative supercoils. Unlike topo IV, gyrase cannot unknot and decatenate DNA. Structurally, these two topoisomerases are very similar. One study found that the E. coli CTD of the ParC subunit is a degenerate form of the CTD in gyrase and that it is positioned differently for substrate specificity.
Available Structures
</StructureSection>
References
- ↑ Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR. Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones. Open Biol. 2016 Sep;6(9). pii: rsob.160157. doi: 10.1098/rsob.160157. PMID:27655731 doi:http://dx.doi.org/10.1098/rsob.160157
- ↑ Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR. Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones. Open Biol. 2016 Sep;6(9). pii: rsob.160157. doi: 10.1098/rsob.160157. PMID:27655731 doi:http://dx.doi.org/10.1098/rsob.160157
- ↑ Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport. Nucleic Acids Res. 2013 Aug 21. PMID:23965305 doi:10.1093/nar/gkt749