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1yck

From Proteopedia

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Current revision

Crystal structure of human peptidoglycan recognition protein (PGRP-S)

Structural highlights

1yck is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGRP1_HUMAN 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, and has bacteriostatic activity towards Gram-negative bacteria. Plays a role in innate immunity.^[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

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors of the innate immune system that bind peptidoglycans (PGNs) of bacterial cell walls. These molecules, which are highly conserved from insects to mammals, contribute to host defense against infections by both Gram-positive and Gram-negative bacteria. Here, we present the crystal structure of human PGRP-S at 1.70A resolution. The overall structure of PGRP-S, which participates in intracellular killing of Gram-positive bacteria, is similar to that of other PGRPs, including Drosophila PGRP-LB and PGRP-SA and human PGRP-Ialpha. However, comparison with these PGRPs reveals important differences in both the PGN-binding site and a groove formed by the PGRP-specific segment on the opposite face of the molecule. This groove, which may constitute a binding site for effector or signaling proteins, is less hydrophobic and deeper in PGRP-S than in PGRP-IalphaC, whose PGRP-specific segments vary considerably in amino acid sequence. By docking a PGN ligand into the PGN-binding cleft of PGRP-S based on the known structure of a PGRP-Ialpha-PGN complex, we identified potential PGN-binding residues in PGRP-S. Differences in PGN-contacting residues and interactions suggest that, although PGRPs may engage PGNs in a similar mode, structural differences exist that likely regulate the affinity and fine specificity of PGN recognition.

Crystal structure of human peptidoglycan recognition protein S (PGRP-S) at 1.70 A resolution.,Guan R, Wang Q, Sundberg EJ, Mariuzza RA J Mol Biol. 2005 Apr 8;347(4):683-91. PMID:15769462^[3]

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

References

↑ Liu C, Xu Z, Gupta D, Dziarski R. Peptidoglycan recognition proteins: a novel family of four human innate immunity pattern recognition molecules. J Biol Chem. 2001 Sep 14;276(37):34686-94. Epub 2001 Jul 18. PMID:11461926 doi:http://dx.doi.org/10.1074/jbc.M105566200
↑ Lu X, Wang M, Qi J, Wang H, Li X, Gupta D, Dziarski R. Peptidoglycan recognition proteins are a new class of human bactericidal proteins. J Biol Chem. 2006 Mar 3;281(9):5895-907. Epub 2005 Dec 14. PMID:16354652 doi:http://dx.doi.org/10.1074/jbc.M511631200
↑ Guan R, Wang Q, Sundberg EJ, Mariuzza RA. Crystal structure of human peptidoglycan recognition protein S (PGRP-S) at 1.70 A resolution. J Mol Biol. 2005 Apr 8;347(4):683-91. PMID:15769462 doi:10.1016/j.jmb.2005.01.070

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/1yck"

@@ Line 1: / Line 1: @@
 ==Crystal structure of human peptidoglycan recognition protein (PGRP-S)==
-<StructureSection load='1yck' size='340' side='right' caption='[[1yck]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='1yck' size='340' side='right'caption='[[1yck]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yck]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yck]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YCK FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1sk3|1sk3]], [[1sk4|1sk4]], [[1twq|1twq]], [[1oht|1oht]], [[1s2j|1s2j]], [[1sxr|1sxr]]</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]] 1.7&#8491;</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=1yck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yck OCA], [http://pdbe.org/1yck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yck RCSB], [http://www.ebi.ac.uk/pdbsum/1yck 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=1yck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yck OCA], [https://pdbe.org/1yck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yck RCSB], [https://www.ebi.ac.uk/pdbsum/1yck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yck ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PGRP1_HUMAN PGRP1_HUMAN]] 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, and has bacteriostatic activity towards Gram-negative bacteria. Plays a role in innate immunity.<ref>PMID:11461926</ref> <ref>PMID:16354652</ref>
+[https://www.uniprot.org/uniprot/PGRP1_HUMAN PGRP1_HUMAN] 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, and has bacteriostatic activity towards Gram-negative bacteria. Plays a role in innate immunity.<ref>PMID:11461926</ref> <ref>PMID:16354652</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/yc/1yck_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yc/1yck_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1yck ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Guan, R]]
+[[Category: Large Structures]]
-[[Category: Mariuzza, R A]]
+[[Category: Guan R]]
-[[Category: Sundberg, E J]]
+[[Category: Mariuzza RA]]
-[[Category: Wang, Q]]
+[[Category: Sundberg EJ]]
-[[Category: Immune system]]
+[[Category: Wang Q]]
-[[Category: Innate immunity]]
-[[Category: Pattern recognition protein]]
-[[Category: Peptidoglycan recognition]]
-[[Category: Pgrp-]]

1yck

From Proteopedia

Current revision

Crystal structure of human peptidoglycan recognition protein (PGRP-S)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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