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2g9e

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Protonation-mediated structural flexibility in the F conjugation regulatory protein, TRAM

Structural highlights

2g9e is a 1 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 1.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRAM1_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. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.^[1] ^[2] ^[3] ^[4]

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

TraM is essential for F plasmid-mediated bacterial conjugation, where it binds to the plasmid DNA near the origin of transfer, and recognizes a component of the transmembrane DNA transfer complex, TraD. Here we report the 1.40 A crystal structure of the TraM core tetramer (TraM58-127). TraM58-127 is a compact eight-helical bundle, in which the N-terminal helices from each protomer interact to form a central, parallel four-stranded coiled-coil, whereas each C-terminal helix packs in an antiparallel arrangement around the outside of the structure. Four protonated glutamic acid residues (Glu88) are packed in a hydrogen-bonded arrangement within the central four-helix bundle. Mutational and biophysical analyses indicate that this protonated state is in equilibrium with a deprotonated tetrameric form characterized by a lower helical content at physiological pH and temperature. Comparison of TraM to its Glu88 mutants predicted to stabilize the helical structure suggests that the protonated state is the active form for binding TraD in conjugation.

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM.,Lu J, Edwards RA, Wong JJ, Manchak J, Scott PG, Frost LS, Glover JN EMBO J. 2006 Jun 21;25(12):2930-9. Epub 2006 May 18. PMID:16710295^[5]

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

References

↑ Di Laurenzio L, Frost LS, Paranchych W. The TraM protein of the conjugative plasmid F binds to the origin of transfer of the F and ColE1 plasmids. Mol Microbiol. 1992 Oct;6(20):2951-9. PMID:1479887
↑ Penfold SS, Simon J, Frost LS. Regulation of the expression of the traM gene of the F sex factor of Escherichia coli. Mol Microbiol. 1996 May;20(3):549-58. PMID:8736534
↑ Fekete RA, Frost LS. Characterizing the DNA contacts and cooperative binding of F plasmid TraM to its cognate sites at oriT. J Biol Chem. 2002 May 10;277(19):16705-11. Epub 2002 Mar 1. PMID:11875064 doi:http://dx.doi.org/10.1074/jbc.M111682200
↑ Ragonese H, Haisch D, Villareal E, Choi JH, Matson SW. The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI. Mol Microbiol. 2007 Feb;63(4):1173-84. PMID:17238924 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05576.x
↑ Lu J, Edwards RA, Wong JJ, Manchak J, Scott PG, Frost LS, Glover JN. Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM. EMBO J. 2006 Jun 21;25(12):2930-9. Epub 2006 May 18. PMID:16710295

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2g9e"

@@ Line 1: / Line 1: @@
 ==Protonation-mediated structural flexibility in the F conjugation regulatory protein, TRAM==
-<StructureSection load='2g9e' size='340' side='right' caption='[[2g9e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2g9e' size='340' side='right'caption='[[2g9e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2g9e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G9E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G9E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2g9e]] is a 1 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=2G9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G9E FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2g7o|2g7o]]</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]] 1.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">traM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2g9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g9e OCA], [https://pdbe.org/2g9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g9e RCSB], [https://www.ebi.ac.uk/pdbsum/2g9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g9e ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g9e OCA], [http://pdbe.org/2g9e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g9e RCSB], [http://www.ebi.ac.uk/pdbsum/2g9e PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_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. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</ref>
+[https://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_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. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</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/g9/2g9e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g9/2g9e_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2g9e ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Edwards, R A]]
+[[Category: Large Structures]]
-[[Category: Frost, L S]]
+[[Category: Edwards RA]]
-[[Category: Glover, J N]]
+[[Category: Frost LS]]
-[[Category: Lu, J]]
+[[Category: Glover JN]]
-[[Category: Manchak, J]]
+[[Category: Lu J]]
-[[Category: Scott, P G]]
+[[Category: Manchak J]]
-[[Category: Wong, J J]]
+[[Category: Scott PG]]
-[[Category: Dna binding protein]]
+[[Category: Wong JJ]]
-[[Category: E88l mutant]]
-[[Category: Four helix bundle]]
-[[Category: Tetramer]]

2g9e

From Proteopedia

Current revision

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TRAM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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