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| ==RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein, adaptation to peptidoglycan-binding function== | | ==RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein, adaptation to peptidoglycan-binding function== |
| <StructureSection load='4jxb' size='340' side='right' caption='[[4jxb]], [[Resolution|resolution]] 1.56Å' scene=''> | | <StructureSection load='4jxb' size='340' side='right'caption='[[4jxb]], [[Resolution|resolution]] 1.56Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4jxb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_sp._h37rv Mycobacterium sp. h37rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JXB FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4jxb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JXB FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></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]] 1.56Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rv1566c, RVBD_1566c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 Mycobacterium sp. H37Rv])</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></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=4jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jxb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jxb RCSB], [http://www.ebi.ac.uk/pdbsum/4jxb PDBsum]</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=4jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jxb OCA], [https://pdbe.org/4jxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jxb RCSB], [https://www.ebi.ac.uk/pdbsum/4jxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jxb ProSAT]</span></td></tr> |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/O06624_MYCTU O06624_MYCTU] |
| Enzymes carrying NlpC/p60 domains, for instance RipA and RipB from Mycobacterium tuberculosis, are bacterial peptidoglycan hydrolases cleaving the peptide stems and contribute to cell wall remodeling during cell division. A member of this protein family, RipD (Rv1566c) from M. tuberculosis described here, displays sequence alterations in the NlpC/p60 catalytic triad and carries a pentapeptide repeat at its carboxy-terminus. Bioinformatics analysis revealed RipD-like proteins in eleven mycobacterial genomes, while similar pentapeptide-repeats occur in cell wall-localized bacterial proteins and in a mycobacteriophage. In contrast to previously known members of the NlpC/p60 family, RipD does not show peptidoglycan hydrolase activity, which is consistent with the sequence alterations at the catalytic site. A strong interaction of the catalytically inactive core domain with peptidoglycan is however retained, presenting the first example of the NlpC/p60 domains that evolved to a non-catalytic peptidoglycan binding function. Full-length RipD, carrying the C-terminal repeat, shows however a decrease in binding affinity to peptidoglycan, suggesting that the C-terminal tail modulates the interaction with bacterial call wall components. The pentapeptide repeat at the carboxy-terminus does not adopt a defined secondary structure in solution which is in accordance with results from the 1.17A crystal structure of the protein carrying two repeat units.
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| RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.,Both D, Steiner EM, Izumi A, Schneider G, Schnell R Biochem J. 2013 Oct 10. PMID:24107184<ref>PMID:24107184</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Mycobacterium sp. h37rv]] | | [[Category: Large Structures]] |
| [[Category: Both, D]] | | [[Category: Mycobacterium tuberculosis H37Rv]] |
| [[Category: Schneider, G]] | | [[Category: Both D]] |
| [[Category: Schnell, R]] | | [[Category: Schneider G]] |
| [[Category: Steiner, E M]] | | [[Category: Schnell R]] |
| [[Category: Cell invasion]]
| | [[Category: Steiner EM]] |
| [[Category: Cell wall]]
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| [[Category: Envelope biogenesis]]
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| [[Category: Nlpc/p60]]
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