This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2cb3

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of peptidoglycan recognition protein-LE in complex with tracheal cytotoxin (monomeric diaminopimelic acid-type peptidoglycan)

Structural highlights

2cb3 is a 4 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 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGPLE_DROME Peptidoglycan-recognition protein that plays a key role in innate immunity by binding to murein peptidoglycans (PGN) of Gram-negative bacteria and activating the imd/Relish pathway. Has no activity against on Gram-positive bacteria. Binds to diaminopimelic acid-type PGN (DAP-type PGN), an activator of the imd/Relish pathway. Functions synergistically with PGRP-LC in producing resistance to E.coli and B.megaterium infections, which have the DAP-type peptidoglycan. Acts both upstream and in parallel with PGRP-LC in the imd/Relish pathway, and is required for infection-dependent activation of melanization. Required for Relish processing and nuclear translocation following proteolytic cleavage. Its localization suggests a role in the recognition and subsequent activation of the signaling at the first point of contact with invading bacteria.^[1] ^[2]

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

Drosophila peptidoglycan recognition protein (PGRP)-LCx and -LCa are receptors that preferentially recognize meso-diaminopimelic acid (DAP)-type peptidoglycan (PGN) present in Gram-negative bacteria over lysine-type PGN of gram-positive bacteria and initiate the IMD signaling pathway, whereas PGRP-LE plays a synergistic role in this process of innate immune defense. How these receptors can distinguish the two types of PGN remains unclear. Here the structure of the PGRP domain of Drosophila PGRP-LE in complex with tracheal cytotoxin (TCT), the monomeric DAP-type PGN, reveals a buried ionic interaction between the unique carboxyl group of DAP and a previously unrecognized arginine residue. This arginine is conserved in the known DAP-type PGN-interacting PGRPs and contributes significantly to the affinity of the protein for the ligand. Unexpectedly, TCT induces infinite head-to-tail dimerization of PGRP-LE, in which the disaccharide moiety, but not the peptide stem, of TCT is positioned at the dimer interface. A sequence comparison suggests that TCT induces heterodimerization of the ectodomains of PGRP-LCx and -LCa in a closely analogous manner to prime the IMD signaling pathway, except that the heterodimer formation is nonperpetuating.

Structural basis for preferential recognition of diaminopimelic acid-type peptidoglycan by a subset of peptidoglycan recognition proteins.,Lim JH, Kim MS, Kim HE, Yano T, Oshima Y, Aggarwal K, Goldman WE, Silverman N, Kurata S, Oh BH J Biol Chem. 2006 Mar 24;281(12):8286-95. Epub 2006 Jan 20. PMID:16428381^[3]

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

References

↑ Takehana A, Katsuyama T, Yano T, Oshima Y, Takada H, Aigaki T, Kurata S. Overexpression of a pattern-recognition receptor, peptidoglycan-recognition protein-LE, activates imd/relish-mediated antibacterial defense and the prophenoloxidase cascade in Drosophila larvae. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13705-10. PMID:12359879 doi:10.1073/pnas.212301199
↑ Takehana A, Yano T, Mita S, Kotani A, Oshima Y, Kurata S. Peptidoglycan recognition protein (PGRP)-LE and PGRP-LC act synergistically in Drosophila immunity. EMBO J. 2004 Nov 24;23(23):4690-700. PMID:15538387 doi:10.1038/sj.emboj.7600466
↑ Lim JH, Kim MS, Kim HE, Yano T, Oshima Y, Aggarwal K, Goldman WE, Silverman N, Kurata S, Oh BH. Structural basis for preferential recognition of diaminopimelic acid-type peptidoglycan by a subset of peptidoglycan recognition proteins. J Biol Chem. 2006 Mar 24;281(12):8286-95. Epub 2006 Jan 20. PMID:16428381 doi:10.1074/jbc.M513030200

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/2cb3"

Categories: Drosophila melanogaster | Large Structures | Kim M-S | Lim J-H | Oh B-H

@@ Line 3: / Line 3: @@
 <StructureSection load='2cb3' size='340' side='right'caption='[[2cb3]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2cb3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CB3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2cb3]] is a 4 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=2CB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CB3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLD:GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA'>MLD</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]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLD:GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA'>MLD</scene></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=2cb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cb3 OCA], [https://pdbe.org/2cb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cb3 RCSB], [https://www.ebi.ac.uk/pdbsum/2cb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cb3 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGPLE_DROME PGPLE_DROME] Peptidoglycan-recognition protein that plays a key role in innate immunity by binding to murein peptidoglycans (PGN) of Gram-negative bacteria and activating the imd/Relish pathway. Has no activity against on Gram-positive bacteria. Binds to diaminopimelic acid-type PGN (DAP-type PGN), an activator of the imd/Relish pathway. Functions synergistically with PGRP-LC in producing resistance to E.coli and B.megaterium infections, which have the DAP-type peptidoglycan. Acts both upstream and in parallel with PGRP-LC in the imd/Relish pathway, and is required for infection-dependent activation of melanization. Required for Relish processing and nuclear translocation following proteolytic cleavage. Its localization suggests a role in the recognition and subsequent activation of the signaling at the first point of contact with invading bacteria.<ref>PMID:12359879</ref> <ref>PMID:15538387</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Drosophila melanogaster]]
 [[Category: Large Structures]]
-[[Category: Kim, M S]]
+[[Category: Kim M-S]]
-[[Category: Lim, J H]]
+[[Category: Lim J-H]]
-[[Category: Oh, B H]]
+[[Category: Oh B-H]]
-[[Category: Immune system]]
-[[Category: Innate immunity]]
-[[Category: Pgrp]]
-[[Category: Tracheal cytotoxin]]

2cb3

From Proteopedia

Current revision

Crystal structure of peptidoglycan recognition protein-LE in complex with tracheal cytotoxin (monomeric diaminopimelic acid-type peptidoglycan)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox