2a0i: Difference between revisions
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< | ==F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA== | ||
<StructureSection load='2a0i' size='340' side='right'caption='[[2a0i]], [[Resolution|resolution]] 2.72Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2a0i]] 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=2A0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A0I 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]] 2.72Å</td></tr> | |||
--> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2a0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a0i OCA], [https://pdbe.org/2a0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a0i RCSB], [https://www.ebi.ac.uk/pdbsum/2a0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a0i 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/a0/2a0i_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=2a0i ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The TraI protein of conjugative plasmid F factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. TraI36, an N-terminal TraI fragment, binds ssDNA with a subnanomolar K(D) and remarkable sequence specificity. The structure of the TraI36 Y16F variant bound to ssDNA reveals specificity determinants, including a ssDNA intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. Mutagenesis results underscore the intricate design of the binding site, with the greatest effects resulting from substitutions for residues that both contact ssDNA and stabilize protein structure. The active site architecture suggests that the bound divalent cation, which is essential for catalysis, both positions the DNA by liganding two oxygens of the scissile phosphate and increases the partial positive charge on the phosphorus to enhance nucleophilic attack. | |||
Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase.,Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF Structure. 2005 Oct;13(10):1533-44. PMID:16216584<ref>PMID:16216584</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2a0i" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Helicase 3D structures|Helicase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Anderson | [[Category: Large Structures]] | ||
[[Category: Datta | [[Category: Anderson BJ]] | ||
[[Category: Ebie | [[Category: Datta S]] | ||
[[Category: Hargreaves | [[Category: Ebie A]] | ||
[[Category: Harley | [[Category: Hargreaves V]] | ||
[[Category: Larkin | [[Category: Harley MJ]] | ||
[[Category: Schildbach | [[Category: Larkin C]] | ||
[[Category: Schildbach JF]] | |||
Latest revision as of 10:17, 23 August 2023
F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNAF Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA
Structural highlights
FunctionTRAI1_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 PubMedThe TraI protein of conjugative plasmid F factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. TraI36, an N-terminal TraI fragment, binds ssDNA with a subnanomolar K(D) and remarkable sequence specificity. The structure of the TraI36 Y16F variant bound to ssDNA reveals specificity determinants, including a ssDNA intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. Mutagenesis results underscore the intricate design of the binding site, with the greatest effects resulting from substitutions for residues that both contact ssDNA and stabilize protein structure. The active site architecture suggests that the bound divalent cation, which is essential for catalysis, both positions the DNA by liganding two oxygens of the scissile phosphate and increases the partial positive charge on the phosphorus to enhance nucleophilic attack. Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase.,Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF Structure. 2005 Oct;13(10):1533-44. PMID:16216584[11] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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