3c2x: Difference between revisions
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< | ==Crystal structure of peptidoglycan recognition protein at 1.8A resolution== | ||
<StructureSection load='3c2x' size='340' side='right'caption='[[3c2x]], [[Resolution|resolution]] 1.83Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3c2x]] 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=3C2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2X FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83Å</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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=3c2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2x OCA], [https://pdbe.org/3c2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2x RCSB], [https://www.ebi.ac.uk/pdbsum/3c2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2x ProSAT]</span></td></tr> | |||
</table> | |||
== 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 == | |||
[[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/c2/3c2x_consurf.spt"</scriptWhenChecked> | |||
<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/main_output.php?pdb_ID=3c2x ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The mammalian peptidoglycan recognition protein-S (PGRP-S) binds to peptidoglycans (PGNs), which are essential components of the cell wall of bacteria. The protein was isolated from the samples of milk obtained from camels with mastitis and purified to homogeneity and crystallized. The crystals belong to orthorhombic space group I222 with a=87.0 A, b=101.7 A and c=162.3 A having four crystallographically independent molecules in the asymmetric unit. The structure has been determined using X-ray crystallographic data and refined to 1.8 A resolution. Overall, the structures of all the four crystallographically independent molecules are identical. The folding of PGRP-S consists of a central beta-sheet with five beta-strands, four parallel and one antiparallel, and three alpha-helices. This protein fold provides two functional sites. The first of these is the PGN-binding site, located on the groove that opens on the surface in the direction opposite to the location of the N terminus. The second site is implicated to be involved in the binding of non-PGN molecules, it also includes putative N-terminal segment residues (1-31) and helix alpha2 in the extended binding. The structure reveals a novel arrangement of PGRP-S molecules in which two pairs of molecules associate to form two independent dimers. The first dimer is formed by two molecules with N-terminal segments at the interface in which non-PGN binding sites are buried completely, whereas the PGN-binding sites of two participating molecules are fully exposed at the opposite ends of the dimer. In the second dimer, PGN-binding sites are buried at the interface while non-PGN binding sites are fully exposed at the opposite ends of the dimer. This form of dimeric arrangement is unique and seems to be aimed at enhancing the capability of the protein against specific invading bacteria. This mode of functional dimerization enhances efficiency and specificity, and is observed for the first time in the family of PGRP molecules. | |||
Crystal structure of the peptidoglycan recognition protein at 1.8 A resolution reveals dual strategy to combat infection through two independent functional homodimers.,Sharma P, Singh N, Sinha M, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Singh TP J Mol Biol. 2008 May 9;378(4):923-32. Epub 2008 Mar 19. PMID:18395744<ref>PMID:18395744</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3c2x" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Camelus dromedarius]] | [[Category: Camelus dromedarius]] | ||
[[Category: Betzel | [[Category: Large Structures]] | ||
[[Category: Kaur | [[Category: Betzel C]] | ||
[[Category: Perbandt | [[Category: Kaur P]] | ||
[[Category: Sharma | [[Category: Perbandt M]] | ||
[[Category: Sharma | [[Category: Sharma P]] | ||
[[Category: Singh | [[Category: Sharma S]] | ||
[[Category: Singh | [[Category: Singh N]] | ||
[[Category: Sinha | [[Category: Singh TP]] | ||
[[Category: Srinivasan | [[Category: Sinha M]] | ||
[[Category: Srinivasan A]] | |||
Latest revision as of 08:43, 17 October 2024
Crystal structure of peptidoglycan recognition protein at 1.8A resolutionCrystal structure of peptidoglycan recognition protein at 1.8A 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 PubMedThe mammalian peptidoglycan recognition protein-S (PGRP-S) binds to peptidoglycans (PGNs), which are essential components of the cell wall of bacteria. The protein was isolated from the samples of milk obtained from camels with mastitis and purified to homogeneity and crystallized. The crystals belong to orthorhombic space group I222 with a=87.0 A, b=101.7 A and c=162.3 A having four crystallographically independent molecules in the asymmetric unit. The structure has been determined using X-ray crystallographic data and refined to 1.8 A resolution. Overall, the structures of all the four crystallographically independent molecules are identical. The folding of PGRP-S consists of a central beta-sheet with five beta-strands, four parallel and one antiparallel, and three alpha-helices. This protein fold provides two functional sites. The first of these is the PGN-binding site, located on the groove that opens on the surface in the direction opposite to the location of the N terminus. The second site is implicated to be involved in the binding of non-PGN molecules, it also includes putative N-terminal segment residues (1-31) and helix alpha2 in the extended binding. The structure reveals a novel arrangement of PGRP-S molecules in which two pairs of molecules associate to form two independent dimers. The first dimer is formed by two molecules with N-terminal segments at the interface in which non-PGN binding sites are buried completely, whereas the PGN-binding sites of two participating molecules are fully exposed at the opposite ends of the dimer. In the second dimer, PGN-binding sites are buried at the interface while non-PGN binding sites are fully exposed at the opposite ends of the dimer. This form of dimeric arrangement is unique and seems to be aimed at enhancing the capability of the protein against specific invading bacteria. This mode of functional dimerization enhances efficiency and specificity, and is observed for the first time in the family of PGRP molecules. Crystal structure of the peptidoglycan recognition protein at 1.8 A resolution reveals dual strategy to combat infection through two independent functional homodimers.,Sharma P, Singh N, Sinha M, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Singh TP J Mol Biol. 2008 May 9;378(4):923-32. Epub 2008 Mar 19. PMID:18395744[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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