1p4d: Difference between revisions

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-[[Image:1p4d.gif|left|200px]]<br /><applet load="1p4d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1p4d, resolution 2.60&Aring;" />
-'''F factor TraI Relaxase Domain'''<br />
-==Overview==
+==F factor TraI Relaxase Domain==
-Conjugative plasmid transfer between bacteria disseminates antibiotic resistance and diversifies prokaryotic genomes. Relaxases, proteins essential for conjugation, cleave one plasmid strand sequence specifically prior to transfer. Cleavage occurs through a Mg(2+)-dependent transesterification involving a tyrosyl hydroxyl and a DNA phosphate. The structure of the F plasmid TraI relaxase domain, described here, is a five-strand beta sheet flanked by alpha helices. The protein resembles replication initiator protein AAV-5 Rep but is circularly permuted, yielding a different topology. The beta sheet forms a binding cleft lined with neutral, nonaromatic residues, unlike most single-stranded DNA binding proteins which use aromatic and charged residues. The cleft contains depressions, suggesting base recognition occurs in a knob-into-hole fashion. Unlike most nucleases, three histidines but no acidic residues coordinate a Mg(2+) located near the catalytic tyrosine. The full positive charge on the Mg(2+) and the architecture of the active site suggest multiple roles for Mg(2+) in DNA cleavage.
+<StructureSection load='1p4d' size='340' side='right'caption='[[1p4d]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1p4d]] is a 3 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=1P4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4D 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]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=1p4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4d OCA], [https://pdbe.org/1p4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4d RCSB], [https://www.ebi.ac.uk/pdbsum/1p4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4d 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/p4/1p4d_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=1p4d ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-P4D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4D OCA].
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structural insights into single-stranded DNA binding and cleavage by F factor TraI., Datta S, Larkin C, Schildbach JF, Structure. 2003 Nov;11(11):1369-79. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14604527 14604527]
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Datta, S.]]
+[[Category: Datta S]]
-[[Category: Larkin, C.]]
+[[Category: Larkin C]]
-[[Category: Schildbach, J F.]]
+[[Category: Schildbach JF]]
-[[Category: EDO]]
-[[Category: MG]]
-[[Category: 3 histidine mg(ii) coordination]]
-[[Category: 5-strand antiparallel beta sheet]]
-[[Category: alpha-beta]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:24:57 2008''