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| | ==Solution structure of the C domain of RV0899 from mycobacterium tuberculosis== | | ==Solution structure of the C domain of RV0899 from mycobacterium tuberculosis== |
| - | <StructureSection load='2lca' size='340' side='right' caption='[[2lca]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2lca' size='340' side='right'caption='[[2lca]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2lca]] 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=2LCA OCA]. <br> | + | <table><tr><td colspan='2'>[[2lca]] 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=2LCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LCA FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rv0899, MT0922, MTCY31.27 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=2lca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lca OCA], [https://pdbe.org/2lca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lca RCSB], [https://www.ebi.ac.uk/pdbsum/2lca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lca ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lca RCSB], [http://www.ebi.ac.uk/pdbsum/2lca PDBsum]</span></td></tr> | + | </table> |
| - | <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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | Molecular Structure and Peptidoglycan Recognition of Mycobacterium tuberculosis ArfA (Rv0899).,Yao Y, Barghava N, Kim J, Niederweis M, Marassi FM J Mol Biol. 2012 Feb 17;416(2):208-20. Epub 2011 Dec 21. PMID:22206986<ref>PMID:22206986</ref> | | Molecular Structure and Peptidoglycan Recognition of Mycobacterium tuberculosis ArfA (Rv0899).,Yao Y, Barghava N, Kim J, Niederweis M, Marassi FM J Mol Biol. 2012 Feb 17;416(2):208-20. Epub 2011 Dec 21. PMID:22206986<ref>PMID:22206986</ref> |
| | | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2lca" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Mycobacterium tuberculosis]] | | [[Category: Mycobacterium tuberculosis]] |
| - | [[Category: Marassi, F.]] | + | [[Category: Marassi F]] |
| - | [[Category: Yao, Y.]] | + | [[Category: Yao Y]] |
| - | [[Category: Peptidoglycan-binding protein]]
| + | |
| Structural highlights
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]
Publication Abstract from PubMed
Mycobacterium tuberculosis ArfA (Rv0899) is a membrane protein encoded by an operon that is required for supporting bacterial growth in acidic environments. Its C-terminal domain (C domain) shares significant sequence homology with the OmpA-like family of peptidoglycan-binding domains, suggesting that its physiological function in acid stress protection may be related to its interaction with the mycobacterial cell wall. Previously, we showed that ArfA forms three independently structured modules, and we reported the structure of its central domain (B domain). Here, we describe the high-resolution structure and dynamics of the C domain, we identify ArfA as a peptidoglycan-binding protein and we elucidate the molecular basis for its specific recognition of diaminopimelate-type peptidoglycan. The C domain of ArfA adopts the characteristic fold of the OmpA-like family. It exhibits pH-dependent conformational dynamics (with significant heterogeneity at neutral pH and a more ordered structure at acidic pH), which could be related to its acid stress response. The C domain associates tightly with polymeric peptidoglycan isolated from M. tuberculosis and also associates with a soluble peptide intermediate of peptidoglycan biosynthesis. This enabled us to characterize the peptidoglycan binding site where five highly conserved ArfA residues, including two key arginines, establish the specificity for diaminopimelate- but not Lys-type peptidoglycan. ArfA is the first peptidoglycan-binding protein to be identified in M. tuberculosis. Its functions in acid stress protection and peptidoglycan binding suggest a link between the acid stress response and the physicochemical properties of the mycobacterial cell wall.
Molecular Structure and Peptidoglycan Recognition of Mycobacterium tuberculosis ArfA (Rv0899).,Yao Y, Barghava N, Kim J, Niederweis M, Marassi FM J Mol Biol. 2012 Feb 17;416(2):208-20. Epub 2011 Dec 21. PMID:22206986[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
- ↑ Yao Y, Barghava N, Kim J, Niederweis M, Marassi FM. Molecular Structure and Peptidoglycan Recognition of Mycobacterium tuberculosis ArfA (Rv0899). J Mol Biol. 2012 Feb 17;416(2):208-20. Epub 2011 Dec 21. PMID:22206986 doi:10.1016/j.jmb.2011.12.030
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