4ebs - Revision history

OCA: Replacing page with 'REMOVED: The PDB entry 4ebs was removed.'

2015-08-20T12:09:02Z

Replacing page with 'REMOVED: The PDB entry 4ebs was removed.'

← Older revision		Revision as of 12:09, 20 August 2015
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	~~==Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid==~~		REMOVED: The PDB entry 4ebs was removed.
	~~<StructureSection load='4ebs' size='340' side='right' caption='[[4ebs]], [[Resolution\|resolution]] 2.60Å' scene=''>~~
	~~== Structural highlights ==~~
	~~<table><tr><td colspan='2'>[[4ebs]] is a 4 chain structure with sequence from [http~~://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMU:BETA-N-ACETYLMURAMIC+ACID'>AMU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ebt\|4ebt]]</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=4ebs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ebs RCSB], [http://www.ebi.ac.uk/pdbsum/4ebs ~~PDBsum]</span></td></tr>~~
	~~</table>~~
	~~== Function ==~~
	[[http://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).
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Peptidoglycan (PGN) consists of repeating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), which are cross-linked by short peptides. It is well known that PGN forms a major cell wall component of bacteria making it an important ligand for the recognition by peptidoglycan recognition proteins (PGRPs) of the host. The binding studies showed that PGN, GlcNAc, and MurNAc bind to camel PGRP-S (CPGRP-S) with affinities corresponding to dissociation constants of 1.3 x 10(-9), 2.6 x 10(-7), and 1.8 x 10(-7) M, respectively. The crystal structure determinations of the complexes of CPGRP-S with GlcNAc and MurNAc showed that the structures consist of four crystallographically independent molecules, A, B, C, and D, in the asymmetric unit that exists as A-B and C-D units of two neighboring linear polymers. The structure determinations showed that compounds GlcNAc and MurNAc bound to CPGRP-S at the same subsite in molecule C. Both GlcNAc and MurNAc form several hydrogen bonds and extensive hydrophobic interactions with protein atoms, indicating the specific nature of their bindings. Flow cytometric studies showed that PGN enhanced the secretions of TNF-alpha and IL-6 from human peripheral blood mononuclear cells. The introduction of CPGRP-S to the PGN-challenged cultured peripheral blood mononuclear cells reduced the expressions of proinflammatory cytokines, TNF-alpha and IL-6. This showed that CPGRP-S inhibited PGN-induced production of proinflammatory cytokines and down-regulated macrophage-mediated inflammation, indicating its potential applications as an antibacterial agent.

	Structural studies on molecular interactions between camel peptidoglycan recognition protein, CPGRP-S, and peptidoglycan moieties N-acetylglucosamine and N-acetylmuramic acid.,Sharma P, Yamini S, Dube D, Singh A, Sinha M, Dey S, Mitra DK, Kaur P, Sharma S, Singh TP J Biol Chem. 2012 Jun 22;287(26):22153-64. Epub 2012 May 9. PMID:22573327<ref>PMID:22573327</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine~~.~~<br>~~
	~~</div>~~
	~~== References ==~~
	~~<references/>~~
	~~__TOC__~~
	~~</StructureSection>~~
	~~[[Category: Camelus dromedarius]]~~
	~~[[Category: Dube, D]]~~
	~~[[Category: Kaur, P]]~~
	~~[[Category: Sharma, P]]~~
	~~[[Category: Sharma, S]]~~
	~~[[Category: Singh, T P]]~~
	~~[[Category: Sinha, M]]~~
	~~[[Category: Yamini, S]]~~
	~~[[Category: Antibiotic]]~~
	~~[[Category: Antimicrobial]]~~
	~~[[Category: Immune response]]~~
	~~[[Category: Immune system]]~~
	~~[[Category: Peptidoglycan binding]]~~
	~~[[Category: Pgrp]]~~
	~~[[Category: Secreted]]~~

OCA at 14:42, 25 December 2014

2014-12-25T14:42:03Z

← Older revision		Revision as of 14:42, 25 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ebs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ebs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBS FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMU:BETA-N-ACETYLMURAMIC+ACID'>AMU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMU:BETA-N-ACETYLMURAMIC+ACID'>AMU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ebt\|4ebt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ebt\|4ebt]]</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=4ebs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ebs RCSB], [http://www.ebi.ac.uk/pdbsum/4ebs PDBsum]</span></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=4ebs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ebs RCSB], [http://www.ebi.ac.uk/pdbsum/4ebs PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://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).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Camelus dromedarius]]		[[Category: Camelus dromedarius]]
	[[Category: Dube, D.]]		[[Category: Dube, D]]
	[[Category: Kaur, P.]]		[[Category: Kaur, P]]
	[[Category: Sharma, P.]]		[[Category: Sharma, P]]
	[[Category: Sharma, S.]]		[[Category: Sharma, S]]
	[[Category: Singh, T P.]]		[[Category: Singh, T P]]
	[[Category: Sinha, M.]]		[[Category: Sinha, M]]
	[[Category: Yamini, S.]]		[[Category: Yamini, S]]
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]

OCA at 10:26, 16 June 2014

2014-06-16T10:26:15Z

← Older revision		Revision as of 10:26, 16 June 2014
Line 1:		Line 1:
	[[~~Image~~:~~4ebs~~.~~png~~\|~~left~~\|~~200px~~]]		==Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid==
			<StructureSection load='4ebs' size='340' side='right' caption='[[4ebs]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4ebs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EBS FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMU:BETA-N-ACETYLMURAMIC+ACID'>AMU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ebt\|4ebt]]</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=4ebs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ebs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ebs RCSB], [http://www.ebi.ac.uk/pdbsum/4ebs PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Peptidoglycan (PGN) consists of repeating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), which are cross-linked by short peptides. It is well known that PGN forms a major cell wall component of bacteria making it an important ligand for the recognition by peptidoglycan recognition proteins (PGRPs) of the host. The binding studies showed that PGN, GlcNAc, and MurNAc bind to camel PGRP-S (CPGRP-S) with affinities corresponding to dissociation constants of 1.3 x 10(-9), 2.6 x 10(-7), and 1.8 x 10(-7) M, respectively. The crystal structure determinations of the complexes of CPGRP-S with GlcNAc and MurNAc showed that the structures consist of four crystallographically independent molecules, A, B, C, and D, in the asymmetric unit that exists as A-B and C-D units of two neighboring linear polymers. The structure determinations showed that compounds GlcNAc and MurNAc bound to CPGRP-S at the same subsite in molecule C. Both GlcNAc and MurNAc form several hydrogen bonds and extensive hydrophobic interactions with protein atoms, indicating the specific nature of their bindings. Flow cytometric studies showed that PGN enhanced the secretions of TNF-alpha and IL-6 from human peripheral blood mononuclear cells. The introduction of CPGRP-S to the PGN-challenged cultured peripheral blood mononuclear cells reduced the expressions of proinflammatory cytokines, TNF-alpha and IL-6. This showed that CPGRP-S inhibited PGN-induced production of proinflammatory cytokines and down-regulated macrophage-mediated inflammation, indicating its potential applications as an antibacterial agent.

	~~{{STRUCTURE_4ebs\| PDB=4ebs \| SCENE= }}~~		Structural studies on molecular interactions between camel peptidoglycan recognition protein, CPGRP-S, and peptidoglycan moieties N-acetylglucosamine and N-acetylmuramic acid.,Sharma P, Yamini S, Dube D, Singh A, Sinha M, Dey S, Mitra DK, Kaur P, Sharma S, Singh TP J Biol Chem. 2012 Jun 22;287(26):22153-64. Epub 2012 May 9. PMID:22573327<ref>PMID:22573327</ref>

	~~===Structural studies on~~ the ~~molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-~~S ~~and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22573327}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[4ebs]] is a 4 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EBS OCA].~~		</StructureSection>
	[[Category: Camelus dromedarius]]		[[Category: Camelus dromedarius]]
	[[Category: Dube, D.]]		[[Category: Dube, D.]]

OCA at 05:15, 12 September 2012

2012-09-12T05:15:04Z

← Older revision		Revision as of 05:15, 12 September 2012
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	[[Image:4ebs.~~jpg~~\|left\|200px]]		[[Image:4ebs.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_4ebs", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
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	{{STRUCTURE_4ebs\| PDB=4ebs \| SCENE= }}		{{STRUCTURE_4ebs\| PDB=4ebs \| SCENE= }}

	===Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid===		===Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid===

			{{ABSTRACT_PUBMED_22573327}}

	==About this Structure==		==About this Structure==

OCA at 07:13, 11 April 2012

2012-04-11T07:13:45Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4ebs.jpg|left|200px]]
-The entry 4ebs is ON HOLD
+<!--
-Authors: Sharma, P., Yamini, S., Dube, D., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
+===Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid===
-Description: Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid

OCA: Protected "4ebs" [edit=sysop:move=sysop]

2012-04-04T05:47:45Z

Protected "4ebs" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:47, 4 April 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4ebs is ON HOLD Authors: Sharma, P., Yamini, S., Dube, D., Sinha, M., Kaur, P., Sharma, S., Singh, T.P. Description: Structural studies on the mole...

2012-04-04T05:47:44Z

New page: '''Unreleased structure''' The entry 4ebs is ON HOLD Authors: Sharma, P., Yamini, S., Dube, D., Sinha, M., Kaur, P., Sharma, S., Singh, T.P. Description: Structural studies on the mole...

New page

'''Unreleased structure'''

The entry 4ebs is ON HOLD

Authors: Sharma, P., Yamini, S., Dube, D., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Description: Structural studies on the molecular interactions between camel Peptidoglycan Recognition Protein, CPGRP-S and peptidoglycan moieties, N-Acetylglucosamine and N-Acetylmuramic acid