4jxb: Difference between revisions

Line 1:

~~{{STRUCTURE_4jxb| PDB=4jxb | SCENE= }}~~

==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===

~~{{ABSTRACT_PUBMED_24107184}}~~

== 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>

</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>

<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='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>

</table>

== Publication Abstract from PubMed ==

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.

~~==About this Structure==~~

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>

~~[[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].~~

==~~Reference~~==

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

~~<ref group="xtra">PMID:024107184</ref>~~<references ~~group="xtra"~~/><~~references~~/>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Mycobacterium sp. h37rv]]

[[Category: Both, D.]]

[[Category: Both, D]]

[[Category: Schneider, G.]]

[[Category: Schneider, G]]

[[Category: Schnell, R.]]

[[Category: Schnell, R]]

[[Category: Steiner, E M.]]

[[Category: Steiner, E M]]

[[Category: Cell invasion]]

[[Category: Cell wall]]

[[Category: Envelope biogenesis]]

[[Category: Nlpc/p60]]

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@@ Line 1: / Line 1: @@
-{{STRUCTURE_4jxb|  PDB=4jxb  |  SCENE=  }}
+==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]] 1.56&Aring;' scene=''>
-{{ABSTRACT_PUBMED_24107184}}
+== 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>
+</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>
+<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='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>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==About this Structure==
+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>
-[[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].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:024107184</ref><references group="xtra"/><references/>
+</div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Mycobacterium sp. h37rv]]
-[[Category: Both, D.]]
+[[Category: Both, D]]
-[[Category: Schneider, G.]]
+[[Category: Schneider, G]]
-[[Category: Schnell, R.]]
+[[Category: Schnell, R]]
-[[Category: Steiner, E M.]]
+[[Category: Steiner, E M]]
 [[Category: Cell invasion]]
 [[Category: Cell wall]]
 [[Category: Envelope biogenesis]]
 [[Category: Nlpc/p60]]