User:Fadel A. Samatey/FlhBc I: Difference between revisions
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<span style="font-size:160%"><b>Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins.</b></span><br><br> | <span style="font-size:160%"><b>Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins.</b></span><br><br> | ||
<span style="font-size:120%">Vladimir A. Meshcheryakov, Akio Kitao, Hideyuki Matsunami and [[Fadel A. Samatey Group|Fadel A. Samatey]] ([[Fadel A. Samatey Group (Japanese)|サマテ]]). ''Acta Cryst. D69: 812-820 (2013). [http://dx.doi.org/10.1107/S0907444913002102 doi:10.1107/S0907444913002102]</span> | <span style="font-size:120%">Vladimir A. Meshcheryakov, Akio Kitao, Hideyuki Matsunami and [[Fadel A. Samatey Group|Fadel A. Samatey]] ([[Fadel A. Samatey Group (Japanese)|サマテ]]). ''Acta Cryst. D69: 812-820 (2013). [http://dx.doi.org/10.1107/S0907444913002102 doi:10.1107/S0907444913002102] <span style="background-color:#ffff80;padding:3px;"><i>Open Access.</i></span></span> | ||
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Contact: [[Image:Samatey-email-address.png|160px]] | |||
===Brief Introduction=== | ===Brief Introduction=== | ||
FlhB is a membrane protein that is part of the flagellum-specific secretion apparatus. It is required for secretion of flagellar proteins, and for bacterial motility. FlhB is paralogous to a protein in the virulence type III secretion system. FlhB has a hydrophobic integral membrane domain, predicted to have four transmembrane helices, a flexible linker that is highly conserved and essential for function, and a cytoplasmic domain. The present study reports the structures of the cytoplasmic domains of two bacterial taxa. | FlhB is a membrane protein that is part of the flagellum-specific secretion apparatus. It is required for secretion of flagellar proteins, and for bacterial motility. FlhB is paralogous to a protein in the virulence type III secretion system. FlhB has a hydrophobic integral membrane domain, predicted to have four transmembrane helices, a flexible linker that is highly conserved and essential for function, and a cytoplasmic domain. The present study reports the structures of the cytoplasmic domains of two bacterial taxa. | ||
(Please see [http://dx.doi.org/10.1107/S0907444913002102 the publication] for a more detailed introduction.) | (Please see [http://dx.doi.org/10.1107/S0907444913002102 the open access publication] for a more detailed introduction.) | ||
==Molecular Tour: FlhBc Structures== | ==Molecular Tour: FlhBc Structures== | ||
<StructureSection size=' | <!--<StructureSection size='400' frame='true' align='right' caption='Cytoplasmic domain of FlhB' scene='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6' >--> | ||
<table cellpadding="6" style="background-color:#ffff80"><tr><td> | <StructureSection load='' size='400' side='right' caption='Cytoplasmic domain of FlhB' scene='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6'> | ||
<!--<table cellpadding="6" style="background-color:#ffff80"><tr><td> | |||
This page is under construction. We expect to complete additional interactive molecular scenes before May 5, 2013. | This page is under construction. We expect to complete additional interactive molecular scenes before May 5, 2013. | ||
</td></tr></table> | </td></tr></table>--> | ||
===''Salmonella''=== | |||
FlhB from ''Salmonella typhimurium'' consists of 383 amino acids. The cytoplasmic domain 219-383 (length 165, 43% of full length) was crystallized. The resulting model [[3b0z]] includes coordinates for residues 229-353 (length 125, 76% of the crystallized length). The [[asymmetric unit]] contains a single molecule (<scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6'>restore initial scene</scene>). | FlhB from ''Salmonella typhimurium'' consists of 383 amino acids. The cytoplasmic domain 219-383 (length 165, 43% of full length) was crystallized. The resulting model [[3b0z]] includes coordinates for residues 229-353 (length 125, 76% of the crystallized length). The [[asymmetric unit]] contains a single molecule (<scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6'>restore initial scene</scene>). | ||
<center><span style="background-color:black;padding:4px;">{{Template:ColorKey_Helix}}, | <center><span style="background-color:black;padding:4px;">{{Template:ColorKey_Helix}}, | ||
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{{Template:ColorKey_N2CRainbow}} | {{Template:ColorKey_N2CRainbow}} | ||
===''Aquifex''=== | |||
FlhB from the thermophile<ref>[http://en.wikipedia.org/wiki/Aquifex_aeolicus Optimum growth ~90<sup>o</sup> C].</ref> ''Aquifex aeolicus'' is shorter, 350 residues (vs. 383 for ''S. typhimurium''), with 32% sequence identity. Residues 213-350 (length 138) were crystallized, and the resulting model [[3b1s]] has <scene name='User:Fadel_A._Samatey/FlhBc_I/Triple-au-aquifex/1'>three molecules</scene> in the [[asymmetric unit]]. The molecule displayed in the comparison in the next section, with chains designated C and D, was chosen because it has the lowest average [[temperature factor]] (66.2, vs. 84.7 and 72.6 for A,B and E,F respectively). It has coordinates for 232-337 (length 106, 77% of the crystallized segment), cleaved at NPTH between Asn263 and Pro264. | FlhB from the thermophile<ref>[http://en.wikipedia.org/wiki/Aquifex_aeolicus Optimum growth ~90<sup>o</sup> C].</ref> ''Aquifex aeolicus'' is shorter, 350 residues (vs. 383 for ''S. typhimurium''), with 32% sequence identity. Residues 213-350 (length 138) were crystallized, and the resulting model [[3b1s]] has <scene name='User:Fadel_A._Samatey/FlhBc_I/Triple-au-aquifex/1'>three molecules</scene> in the [[asymmetric unit]]. The molecule displayed in the comparison in the next section, with chains designated C and D, was chosen because it has the lowest average [[temperature factor]] (66.2, vs. 84.7 and 72.6 for A,B and E,F respectively). It has coordinates for 232-337 (length 106, 77% of the crystallized segment), cleaved at NPTH between Asn263 and Pro264. | ||
===Comparison=== | |||
The FlhBc ''Salmonella'' <!--<scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st_aa_aligned/2'>-->3D structure is very similar to that of ''Aquifex''. 102 alpha carbons align with an RMSD of 1.0 Å. Their FlhB's have 32% sequence identity. | The FlhBc ''Salmonella'' <!--<scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st_aa_aligned/2'>-->3D structure is very similar to that of ''Aquifex''. 102 alpha carbons align with an RMSD of 1.0 Å. Their FlhB's have 32% sequence identity. | ||
<scene name='User:Fadel_A._Samatey/FlhBc_I/Flhbc_st_plus_aa/2'>Display both structures</scene>, then click the button below to do a structural alignment. | <scene name='User:Fadel_A._Samatey/FlhBc_I/Flhbc_st_plus_aa/2'>Display both structures</scene>, then click the button below to do a structural alignment. | ||
<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
<script>if ({1.2}.count > 0); compare {1.1} {1.2} SUBSET {*.ca} {246-269:A} {240-263:C} {272-280:B} {266-274:D} {285-351:B} {279-345:D} ATOMS rotate translate; zoomto *1.5;spin y; else; set echo bottom left; color echo white; font echo 20 sansserif;echo "Please display both structures first!"; delay 4; set echo off; endif;</script> | <script>if ({1.2}.count > 0); compare {1.1} {1.2} SUBSET {*.ca} {246-269:A} {240-263:C} {272-280:B} {266-274:D} {285-351:B} {279-345:D} ATOMS rotate translate 3; zoomto *1.5;spin y; else; set echo bottom left; color echo white; font echo 20 sansserif;echo "Please display both structures first!"; delay 4; set echo off; endif;</script> | ||
<text>Do Structural Alignment</text> | <text>Do Structural Alignment</text> | ||
</jmolButton> | </jmolButton> | ||
</jmol> | </jmol> | ||
<center><span style="background-color:black;color:white;padding:4px;"><b><font color="#3030ff">S</font><font color="#30a0ff">al</font><font color="#00ff80">m</font><font color="#00ff00">on</font><font color="#e0ff00">e</font><font color="#ff8000">ll</font><font color="#ff0000">a</font> <font color="#909090">vs.</font> Aquifex</b>.</span></center> | <center><span style="background-color:black;color:white;padding:4px;"><b><font color="#3030ff">S</font><font color="#30a0ff">al</font><font color="#00ff80">m</font><font color="#00ff00">on</font><font color="#e0ff00">e</font><font color="#ff8000">ll</font><font color="#ff0000">a</font> <font color="#909090">vs.</font> Aquifex</b>.</span></center> | ||
===Charge=== | |||
The <scene name='User:Fadel_A._Samatey/FlhBc_I/Charge_st/2'>charges on the surface of FlhBc</scene> (''S. typhimurium'') show a cluster of positive charges on one side, referred to in the publication as a "positively charged cleft". | |||
<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}} / <font color='#8080d0'>'''Histidine'''</font></center> | |||
However, only two of the positively charged residues in this cleft region are conserved: Arg320 (ConSurf level 9, maximum), and Arg245 (Consurf level 8). This is shown in another scene below under ''Evolutionary Conservation''. | |||
===Loop 281-285=== | ===Loop 281-285=== | ||
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===Flexibility of N-Terminus=== | ===Flexibility of N-Terminus=== | ||
Molecular dynamics simulations suggested that the mutations in 281-285 reduced flexibility of the N-terminal alpha helix, and hence that such flexibility may be important for function. Indeed, 226-267 (the N-terminal helix is 229 to about 262) is predicted to be intrinsically disordered<ref>Prediction of intrinsic disorder for ''Salmonella typhimurium'' FlhB by the FoldIndex server (image below, at right). [[Image:3b0z-FlhB-foldindex.png|frame]]</ref>. The formation of a helix seems likely to | Molecular dynamics simulations suggested that the mutations in 281-285 reduced flexibility of the N-terminal alpha helix, and hence that such flexibility may be important for function. Indeed, 226-267 (the N-terminal helix is 229 to about 262) is predicted to be intrinsically disordered<ref>Prediction of intrinsic disorder for ''Salmonella typhimurium'' FlhB by the FoldIndex server (image below, at right). [[Image:3b0z-FlhB-foldindex.png|frame]]</ref>. The observed formation of a helix seems likely to depend upon stabilization by crystal contacts mentioned above. | ||
===Evolutionary Conservation=== | ===Evolutionary Conservation=== | ||
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There is a prominent strip of conserved residues on one side of the long N-terminal alpha helix. As mentioned above, the auto-catalytically cleaved segment, including 269 and 270, is highly conserved. In contrast (as mentioned above) the protruding loop 281-285 (which is necessary for function and suggested to be important for flexibility of the N terminus) is not conserved. | There is a prominent strip of conserved residues on one side of the long N-terminal alpha helix. As mentioned above, the auto-catalytically cleaved segment, including 269 and 270, is highly conserved. In contrast (as mentioned above) the protruding loop 281-285 (which is necessary for function and suggested to be important for flexibility of the N terminus) is not conserved. | ||
Conservation of ''A. aeolicus'' FlhBc was similar, especially in the regions mentioned above. | Conservation of ''A. aeolicus'' FlhBc (not shown) was similar, especially in the regions mentioned above. | ||
Turning to the positive charges discussed above, <scene name='User:Fadel_A._Samatey/FlhBc_I/Conservation_st/3'>here only positively charged sidechains (Lys, Arg) are spacefilling. His is depicted in sticks.</scene> All atoms are colored by conservation. With spinning off, touch any sidechain to report its identity. | |||
</StructureSection> | </StructureSection> | ||
===References and Notes=== | ===References and Notes=== | ||
* If you have any comments, questions, or if there is any problem with this page, please contact [[Image:Samatey-email-address.png|150px]]. | |||
<references /> | <references /> | ||
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