2kgw

From Proteopedia

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Current revision

Solution Structure of the carboxy-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis

Structural highlights

2kgw is a 1 chain structure with sequence from Mycobacterium tuberculosis. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 10 models
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARFA_MYCTU Probably plays a role in ammonia secretion that neutralizes the medium at pH 5.5, although it does not play a direct role in ammonia transport. The OmpA-like domain (196-326) binds M.tuberculosis peptidoglycan. Overexpression in M.bovis or M.smegmatis gives channels with average conductance value of 1,600 +/- 100 pS, but this may not be physiologically relevant.^[1] ^[2] ^[3]

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

The pore-forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor required for acid resistance in host phagosomes. In this study, we determined the 3D structure of OmpATb by NMR in solution. We found that OmpATb is composed of two independent domains separated by a proline-rich hinge region. As expected, the high-resolution structure of the C-terminal domain (OmpATb(198-326)) revealed a module structurally related to other OmpA-like proteins from Gram-negative bacteria. The N-terminal domain of OmpATb (73-204), which is sufficient to form channels in planar lipid bilayers, exhibits a fold, which belongs to the alpha+beta sandwich class fold. Its peculiarity is to be composed of two overlapping subdomains linked via a BON (Bacterial OsmY and Nodulation) domain initially identified in bacterial proteins predicted to interact with phospholipids. Although OmpATb(73-204) is highly water soluble, current-voltage measurements demonstrate that it is able to form conducting pores in model membranes. A HADDOCK modeling of the NMR data gathered on the major monomeric form and on the minor oligomeric populations of OmpATb(73-204) suggest that OmpATb(73-204) can form oligomeric rings able to insert into phospholipid membrane, similar to related proteins from the Type III secretion systems, which form multisubunits membrane-associated rings at the basal body of the secretion machinery. Proteins 2010. (c) 2010 Wiley-Liss, Inc.

Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall.,Yang Y, Auguin D, Delbecq S, Dumas E, Molle G, Molle V, Roumestand C, Saint N Proteins. 2010 Oct 12. PMID:21117233^[4]

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

References

↑ Raynaud C, Papavinasasundaram KG, Speight RA, Springer B, Sander P, Bottger EC, Colston MJ, Draper P. The functions of OmpATb, a pore-forming protein of Mycobacterium tuberculosis. Mol Microbiol. 2002 Oct;46(1):191-201. PMID:12366842
↑ Alahari A, Saint N, Campagna S, Molle V, Molle G, Kremer L. The N-terminal domain of OmpATb is required for membrane translocation and pore-forming activity in mycobacteria. J Bacteriol. 2007 Sep;189(17):6351-8. doi: 10.1128/JB.00509-07. Epub 2007 Jun 15. PMID:17573469 doi:http://dx.doi.org/10.1128/JB.00509-07
↑ Song H, Huff J, Janik K, Walter K, Keller C, Ehlers S, Bossmann SH, Niederweis M. Expression of the ompATb operon accelerates ammonia secretion and adaptation of Mycobacterium tuberculosis to acidic environments. Mol Microbiol. 2011 May;80(4):900-18. doi: 10.1111/j.1365-2958.2011.07619.x. Epub, 2011 Mar 16. PMID:21410778 doi:http://dx.doi.org/10.1111/j.1365-2958.2011.07619.x
↑ Yang Y, Auguin D, Delbecq S, Dumas E, Molle G, Molle V, Roumestand C, Saint N. Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall. Proteins. 2010 Oct 12. PMID:21117233 doi:10.1002/prot.22912

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
-[[Image:2kgw.png|left|200px]]
-<!--
+==Solution Structure of the carboxy-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis==
-The line below this paragraph, containing "STRUCTURE_2kgw", creates the "Structure Box" on the page.
+<StructureSection load='2kgw' size='340' side='right'caption='[[2kgw]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2kgw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KGW FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 10 models</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=2kgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kgw OCA], [https://pdbe.org/2kgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kgw RCSB], [https://www.ebi.ac.uk/pdbsum/2kgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kgw ProSAT]</span></td></tr>
-{{STRUCTURE_2kgw|  PDB=2kgw  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARFA_MYCTU ARFA_MYCTU] Probably plays a role in ammonia secretion that neutralizes the medium at pH 5.5, although it does not play a direct role in ammonia transport. The OmpA-like domain (196-326) binds M.tuberculosis peptidoglycan. Overexpression in M.bovis or M.smegmatis gives channels with average conductance value of 1,600 +/- 100 pS, but this may not be physiologically relevant.<ref>PMID:12366842</ref> <ref>PMID:17573469</ref> <ref>PMID:21410778</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/kg/2kgw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2kgw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The pore-forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor required for acid resistance in host phagosomes. In this study, we determined the 3D structure of OmpATb by NMR in solution. We found that OmpATb is composed of two independent domains separated by a proline-rich hinge region. As expected, the high-resolution structure of the C-terminal domain (OmpATb(198-326)) revealed a module structurally related to other OmpA-like proteins from Gram-negative bacteria. The N-terminal domain of OmpATb (73-204), which is sufficient to form channels in planar lipid bilayers, exhibits a fold, which belongs to the alpha+beta sandwich class fold. Its peculiarity is to be composed of two overlapping subdomains linked via a BON (Bacterial OsmY and Nodulation) domain initially identified in bacterial proteins predicted to interact with phospholipids. Although OmpATb(73-204) is highly water soluble, current-voltage measurements demonstrate that it is able to form conducting pores in model membranes. A HADDOCK modeling of the NMR data gathered on the major monomeric form and on the minor oligomeric populations of OmpATb(73-204) suggest that OmpATb(73-204) can form oligomeric rings able to insert into phospholipid membrane, similar to related proteins from the Type III secretion systems, which form multisubunits membrane-associated rings at the basal body of the secretion machinery. Proteins 2010. (c) 2010 Wiley-Liss, Inc.
-===Solution Structure of the carboxy-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis===
+Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall.,Yang Y, Auguin D, Delbecq S, Dumas E, Molle G, Molle V, Roumestand C, Saint N Proteins. 2010 Oct 12. PMID:21117233<ref>PMID:21117233</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2kgw" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21117233}}, adds the Publication Abstract to the page
+*[[Porin 3D structures|Porin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21117233 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21117233}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2kgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KGW OCA].
-==Reference==
-<ref group="xtra">PMID:21117233</ref><references group="xtra"/>
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Auguin, D.]]
+[[Category: Auguin D]]
-[[Category: Delbecq, S.]]
+[[Category: Delbecq S]]
-[[Category: Dumas, E.]]
+[[Category: Dumas E]]
-[[Category: Hoh, F.]]
+[[Category: Hoh F]]
-[[Category: Molle, V.]]
+[[Category: Molle V]]
-[[Category: Saint, N.]]
+[[Category: Saint N]]
-[[Category: Yang, Y.]]
+[[Category: Yang Y]]

2kgw

From Proteopedia

Current revision

Solution Structure of the carboxy-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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