2rkq

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of drosophila peptidoglycan recognition protein SD (PGRP-SD)

Structural highlights

2rkq is a 1 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGPSD_DROME Peptidoglycan-recognition protein that plays a key role in innate immnunity by binding to peptidoglycans (PGN) of Gram-positive bacteria and activating the Toll pathway. Has no activity against on Gram-negative bacteria and fungi. Shows some partial redundancy with PRPGP-SA in Gram-positive bacteria recognition. May act by activating the proteolytic cleavage of Spatzle and the subsequent activation of Toll pathway. Recognizes S.aureus PGN.^[1]

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

In Drosophila the synthesis of antimicrobial peptides in response to microbial infections is under the control of the Toll and immune deficiency (Imd) signaling pathways. The Toll signaling pathway responds mainly to Gram-positive bacterial and fungal infection while the Imd pathway mediates the response to Gram-negative bacteria. Microbial recognition upstream of Toll involves, at least in part, peptidoglycan recognition proteins (PGRPs). The sensing of Gram-positive bacteria is mediated by the pattern recognition receptors PGRP-SA and Gram-negative binding protein 1 (GNBP1) that cooperate to detect the presence of lysine-type peptidoglycan in the host. Recently it has been shown that a loss-of-function mutation in peptidoglycan recognition protein SD (PGRP-SD) severely exacerbates the PGRP-SA and GNBP1 mutant phenotypes. Here we have solved the crystal structure of PGRP-SD at 1.5A resolution. Comparison with available structures of PGRPs in complex with their peptidoglycan (PGN) ligand strongly suggests a diaminopimelic acid (DAP) specificity for PGRP-SD. This result is supported by pull-down assays with insoluble PGNs. In addition we show that Toll pathway activation after infection by DAP-type PGN containing bacteria is clearly reduced in PGRP-SD mutant flies. Our hypothesis is that the role of PGRP-SD is the recognition of DAP-type PGNs responsible for the activation of the Toll pathway by Gram-negative bacteria.

Crystal structure of Drosophila PGRP-SD suggests binding to DAP-type but not lysine-type peptidoglycan.,Leone P, Bischoff V, Kellenberger C, Hetru C, Royet J, Roussel A Mol Immunol. 2008 May;45(9):2521-30. Epub 2008 Mar 4. PMID:18304640^[2]

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

References

↑ Bischoff V, Vignal C, Boneca IG, Michel T, Hoffmann JA, Royet J. Function of the drosophila pattern-recognition receptor PGRP-SD in the detection of Gram-positive bacteria. Nat Immunol. 2004 Nov;5(11):1175-80. Epub 2004 Sep 26. PMID:15448690 doi:http://dx.doi.org/10.1038/ni1123
↑ Leone P, Bischoff V, Kellenberger C, Hetru C, Royet J, Roussel A. Crystal structure of Drosophila PGRP-SD suggests binding to DAP-type but not lysine-type peptidoglycan. Mol Immunol. 2008 May;45(9):2521-30. Epub 2008 Mar 4. PMID:18304640 doi:10.1016/j.molimm.2008.01.015

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of drosophila peptidoglycan recognition protein SD (PGRP-SD)==
-<StructureSection load='2rkq' size='340' side='right' caption='[[2rkq]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='2rkq' size='340' side='right'caption='[[2rkq]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RKQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RKQ FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PGRP-SD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</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]] 1.5&#8491;</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=2rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rkq RCSB], [http://www.ebi.ac.uk/pdbsum/2rkq 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=2rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkq OCA], [https://pdbe.org/2rkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rkq RCSB], [https://www.ebi.ac.uk/pdbsum/2rkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rkq ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGPSD_DROME PGPSD_DROME] Peptidoglycan-recognition protein that plays a key role in innate immnunity by binding to peptidoglycans (PGN) of Gram-positive bacteria and activating the Toll pathway. Has no activity against on Gram-negative bacteria and fungi. Shows some partial redundancy with PRPGP-SA in Gram-positive bacteria recognition. May act by activating the proteolytic cleavage of Spatzle and the subsequent activation of Toll pathway. Recognizes S.aureus PGN.<ref>PMID:15448690</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/rk/2rkq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/2rkq_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2rkq ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2rkq" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 29: / Line 33: @@
 </StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Kellenberger, C.]]
+[[Category: Large Structures]]
-[[Category: Leone, P.]]
+[[Category: Kellenberger C]]
-[[Category: Roussel, A.]]
+[[Category: Leone P]]
-[[Category: Royet, J.]]
+[[Category: Roussel A]]
-[[Category: Drosophila]]
+[[Category: Royet J]]
-[[Category: Glycoprotein]]
-[[Category: Immune response]]
-[[Category: Immune system]]
-[[Category: Innate immunity]]
-[[Category: Pattern recognition]]
-[[Category: Pgrp]]
-[[Category: Secreted]]
-[[Category: Toll]]

2rkq

From Proteopedia

Current revision

Crystal structure of drosophila peptidoglycan recognition protein SD (PGRP-SD)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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