2q7u: Difference between revisions

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{{STRUCTURE_2q7u|  PDB=2q7u  |  SCENE=  }}
'''Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate'''


==Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate==
<StructureSection load='2q7u' size='340' side='right'caption='[[2q7u]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2q7u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q7U FirstGlance]. <br>
</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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PON:IMIDO+DIPHOSPHATE'>PON</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene></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=2q7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q7u OCA], [https://pdbe.org/2q7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q7u RCSB], [https://www.ebi.ac.uk/pdbsum/2q7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q7u ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TRAI1_ECOLI TRAI1_ECOLI] Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Relaxosome formation requires binding of IHF and TraY to the oriT region, which then faciliates binding of TraI relaxase. TraI forms a covalent 5'-phosphotyrosine intermediate linkage to the ssDNA. The transesterified T-strand moves from the donor cell to the recipient cell in a 5'to 3' direction, with the DNA helicase activity of TraI unwinding the DNA. DNA transfer occurs via the conjugative pore (transferosome) an intercellular junction mediated by a type IV secretion system, with TraD providing the means to link the relaxosome to the conjugative pore. The relaxase completes DNA transfer by reversing the covalent phosphotyrosine linkage and releasing the T-strand.<ref>PMID:12637015</ref> <ref>PMID:6308637</ref> <ref>PMID:8386720</ref> <ref>PMID:7499339</ref> <ref>PMID:11560509</ref>  TraI has also been identified as DNA helicase I. DNA. helicase I is a potent, highly processive DNA-dependent ATPase, able to unwind about 1.1 kb dsDNA per second in a 5' to 3' manner.<ref>PMID:12637015</ref> <ref>PMID:6308637</ref> <ref>PMID:8386720</ref> <ref>PMID:7499339</ref> <ref>PMID:11560509</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q7/2q7u_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q7u ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Conjugative transfer of plasmid DNA via close cell-cell junctions is the main route by which antibiotic resistance genes spread between bacterial strains. Relaxases are essential for conjugative transfer and act by cleaving DNA strands and forming covalent phosphotyrosine linkages. Based on data indicating that multityrosine relaxase enzymes can accommodate two phosphotyrosine intermediates within their divalent metal-containing active sites, we hypothesized that bisphosphonates would inhibit relaxase activity and conjugative DNA transfer. We identified bisphosphonates that are nanomolar inhibitors of the F plasmid conjugative relaxase in vitro. Furthermore, we used cell-based assays to demonstrate that these compounds are highly effective at preventing DNA transfer and at selectively killing cells harboring conjugative plasmids. Two potent inhibitors, clodronate and etidronate, are already clinically approved to treat bone loss. Thus, the inhibition of conjugative relaxases is a potentially novel antimicrobial approach, one that selectively targets bacteria capable of transferring antibiotic resistance and generating multidrug resistant strains.


==Overview==
Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase.,Lujan SA, Guogas LM, Ragonese H, Matson SW, Redinbo MR Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12282-7. Epub 2007 Jul 13. PMID:17630285<ref>PMID:17630285</ref>
Conjugative transfer of plasmid DNA via close cell-cell junctions is the main route by which antibiotic resistance genes spread between bacterial strains. Relaxases are essential for conjugative transfer and act by cleaving DNA strands and forming covalent phosphotyrosine linkages. Based on data indicating that multityrosine relaxase enzymes can accommodate two phosphotyrosine intermediates within their divalent metal-containing active sites, we hypothesized that bisphosphonates would inhibit relaxase activity and conjugative DNA transfer. We identified bisphosphonates that are nanomolar inhibitors of the F plasmid conjugative relaxase in vitro. Furthermore, we used cell-based assays to demonstrate that these compounds are highly effective at preventing DNA transfer and at selectively killing cells harboring conjugative plasmids. Two potent inhibitors, clodronate and etidronate, are already clinically approved to treat bone loss. Thus, the inhibition of conjugative relaxases is a potentially novel antimicrobial approach, one that selectively targets bacteria capable of transferring antibiotic resistance and generating multidrug resistant strains.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2Q7U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7U OCA].
</div>
<div class="pdbe-citations 2q7u" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase., Lujan SA, Guogas LM, Ragonese H, Matson SW, Redinbo MR, Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12282-7. Epub 2007 Jul 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17630285 17630285]
*[[Helicase 3D structures|Helicase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Lujan, S A.]]
[[Category: Lujan SA]]
[[Category: Redinbo, M R.]]
[[Category: Redinbo MR]]
[[Category: Alternative initiation]]
[[Category: Atp-binding]]
[[Category: Conjugation]]
[[Category: Dna-binding]]
[[Category: Helicase]]
[[Category: Hydrolase]]
[[Category: Nucleotide-binding]]
[[Category: Plasmid]]
[[Category: Relaxase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 22 21:35:01 2008''

Latest revision as of 14:24, 30 August 2023

Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and ImidodiphosphateCrystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate

Structural highlights

2q7u is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRAI1_ECOLI Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Relaxosome formation requires binding of IHF and TraY to the oriT region, which then faciliates binding of TraI relaxase. TraI forms a covalent 5'-phosphotyrosine intermediate linkage to the ssDNA. The transesterified T-strand moves from the donor cell to the recipient cell in a 5'to 3' direction, with the DNA helicase activity of TraI unwinding the DNA. DNA transfer occurs via the conjugative pore (transferosome) an intercellular junction mediated by a type IV secretion system, with TraD providing the means to link the relaxosome to the conjugative pore. The relaxase completes DNA transfer by reversing the covalent phosphotyrosine linkage and releasing the T-strand.[1] [2] [3] [4] [5] TraI has also been identified as DNA helicase I. DNA. helicase I is a potent, highly processive DNA-dependent ATPase, able to unwind about 1.1 kb dsDNA per second in a 5' to 3' manner.[6] [7] [8] [9] [10]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Conjugative transfer of plasmid DNA via close cell-cell junctions is the main route by which antibiotic resistance genes spread between bacterial strains. Relaxases are essential for conjugative transfer and act by cleaving DNA strands and forming covalent phosphotyrosine linkages. Based on data indicating that multityrosine relaxase enzymes can accommodate two phosphotyrosine intermediates within their divalent metal-containing active sites, we hypothesized that bisphosphonates would inhibit relaxase activity and conjugative DNA transfer. We identified bisphosphonates that are nanomolar inhibitors of the F plasmid conjugative relaxase in vitro. Furthermore, we used cell-based assays to demonstrate that these compounds are highly effective at preventing DNA transfer and at selectively killing cells harboring conjugative plasmids. Two potent inhibitors, clodronate and etidronate, are already clinically approved to treat bone loss. Thus, the inhibition of conjugative relaxases is a potentially novel antimicrobial approach, one that selectively targets bacteria capable of transferring antibiotic resistance and generating multidrug resistant strains.

Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase.,Lujan SA, Guogas LM, Ragonese H, Matson SW, Redinbo MR Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12282-7. Epub 2007 Jul 13. PMID:17630285[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF. Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):86-99. PMID:12637015
  2. ↑ Abdel-Monem M, Taucher-Scholz G, Klinkert MQ. Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4659-63. PMID:6308637
  3. ↑ Matson SW, Nelson WC, Morton BS. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. 1993 May;175(9):2599-606. PMID:8386720
  4. ↑ Nelson WC, Howard MT, Sherman JA, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. 1995 Nov 24;270(47):28374-80. PMID:7499339
  5. ↑ Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry. 2001 Sep 25;40(38):11586-95. PMID:11560509
  6. ↑ Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF. Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):86-99. PMID:12637015
  7. ↑ Abdel-Monem M, Taucher-Scholz G, Klinkert MQ. Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4659-63. PMID:6308637
  8. ↑ Matson SW, Nelson WC, Morton BS. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. 1993 May;175(9):2599-606. PMID:8386720
  9. ↑ Nelson WC, Howard MT, Sherman JA, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. 1995 Nov 24;270(47):28374-80. PMID:7499339
  10. ↑ Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry. 2001 Sep 25;40(38):11586-95. PMID:11560509
  11. ↑ Lujan SA, Guogas LM, Ragonese H, Matson SW, Redinbo MR. Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12282-7. Epub 2007 Jul 13. PMID:17630285

2q7u, resolution 3.00Å

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