3ogx: Difference between revisions
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==Crystal structure of the complex of Peptidoglycan Recognition protein (PGRP-s) with Heparin-Dissacharide at 2.8 A resolution== | ==Crystal structure of the complex of Peptidoglycan Recognition protein (PGRP-s) with Heparin-Dissacharide at 2.8 A resolution== | ||
<StructureSection load='3ogx' size='340' side='right' caption='[[3ogx]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='3ogx' size='340' side='right'caption='[[3ogx]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ogx]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3ogx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OGX FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand= | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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=PRD_900026:HEPARIN+DISACCHARIDE+I-S,'>PRD_900026</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene>, <scene name='pdbligand=UAP:4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>UAP</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=3ogx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ogx OCA], [https://pdbe.org/3ogx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ogx RCSB], [https://www.ebi.ac.uk/pdbsum/3ogx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ogx ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/PGRP1_CAMDR PGRP1_CAMDR] Pattern receptor that binds to murein peptidoglycans (PGN) of Gram-positive bacteria. Has bactericidal activity towards Gram-positive bacteria. May kill Gram-positive bacteria by interfering with peptidoglycan biosynthesis. Binds also to Gram-negative bacteria. Involved in innate immunity. Is microbicidal for Gram-positive and Gram-negative bacteria and yeast. May function in intracellular killing of bacteria (By similarity). | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/3ogx_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/3ogx_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3ogx ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 26: | Line 28: | ||
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 3ogx" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Glutamine | *[[Glutamine synthetase 3D structures|Glutamine synthetase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 34: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Camelus dromedarius]] | [[Category: Camelus dromedarius]] | ||
[[Category: Dube | [[Category: Large Structures]] | ||
[[Category: Kaur | [[Category: Dube D]] | ||
[[Category: Sharma | [[Category: Kaur P]] | ||
[[Category: Sharma | [[Category: Sharma P]] | ||
[[Category: Singh | [[Category: Sharma S]] | ||
[[Category: Sinha | [[Category: Singh TP]] | ||
[[Category: Sinha M]] | |||
Latest revision as of 09:03, 17 October 2024
Crystal structure of the complex of Peptidoglycan Recognition protein (PGRP-s) with Heparin-Dissacharide at 2.8 A resolutionCrystal structure of the complex of Peptidoglycan Recognition protein (PGRP-s) with Heparin-Dissacharide at 2.8 A resolution
Structural highlights
FunctionPGRP1_CAMDR Pattern receptor that binds to murein peptidoglycans (PGN) of Gram-positive bacteria. Has bactericidal activity towards Gram-positive bacteria. May kill Gram-positive bacteria by interfering with peptidoglycan biosynthesis. Binds also to Gram-negative bacteria. Involved in innate immunity. Is microbicidal for Gram-positive and Gram-negative bacteria and yeast. May function in intracellular killing of bacteria (By similarity). 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 PubMedShort peptidoglycan recognition protein (PGRP-S) is a member of the innate immunity system in mammals. PGRP-S from Camelus dromedarius (CPGRP-S) is found to be highly potent against bacterial infections. It is capable of binding to a wide range of pathogen-associated molecular patterns (PAMPs) including lipopolysaccharide (LPS), lipoteichoic acid (LTA) and peptidoglycan (PGN). The heparin-like polysaccharides have also been observed in some bacteria such as the capsule of K5 Escherichia coli thus making them relevant for determining the nature of their interactions with CPGRP-S. The binding studies of CPGRP-S with heparin disaccharide in solution using surface plasmon resonance gave a value 3.3x10(-7) M for the dissociation constant (Kd). The structure of the heparin bound CPGRP-S determined at 2.8A resolution revealed the presence of a bound heparin molecule in the binding pocket of CPGRP-S. It was found anchored tightly to the protein with the help of several ionic and hydrogen bonded interactions. Three sulphate groups of heparin S1, S2 and S3 have been found to interact with residues, Arg-31, Lys-90, Thr- 97, Asn-99 Asn-140, Gln-150 and Arg-170 of CPGRP-S. The binding site includes two subsites, S-I and S-II with cleft-like structures. Heparin disaccharide is bound in subsite S-I. Previously determined structures of the complexes of CPGRP-S with LPS, LTA and PGN also showed that their glycan moieties were also held in subsite S-I indicating that heparin disaccharide also represents an important element for the recognition by CPGRP-S. Structural basis of heparin binding to camel peptidoglycan recognition protein-S.,Sharma P, Dube D, Sinha M, Dey S, Kaur P, Sharma S, Singh TP Int J Biochem Mol Biol. 2012;3(1):86-94. Epub 2012 Mar 20. PMID:22509483[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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