3nkw

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{{STRUCTURE_3nkw| PDB=3nkw | SCENE= }}
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==Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with N-acetyl glucosamine(NAG) at 2.6 A resolution==
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===Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with N-acetyl glucosamine(NAG) at 2.6 A resolution===
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<StructureSection load='3nkw' size='340' side='right' caption='[[3nkw]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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{{ABSTRACT_PUBMED_22573327}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3nkw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c93 3c93]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NKW FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3c2x|3c2x]], [[3cxa|3cxa]]</td></tr>
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<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=3nkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nkw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nkw RCSB], [http://www.ebi.ac.uk/pdbsum/3nkw PDBsum]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/3nkw_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==Function==
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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>
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[[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).
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[3nkw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c93 3c93]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NKW OCA].
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</div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Camelus dromedarius]]
[[Category: Camelus dromedarius]]
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[[Category: Dube, D.]]
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[[Category: Dube, D]]
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[[Category: Kaur, P.]]
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[[Category: Kaur, P]]
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[[Category: Sharma, P.]]
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[[Category: Sharma, P]]
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[[Category: Sharma, S.]]
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[[Category: Sharma, S]]
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[[Category: Singh, T P.]]
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[[Category: Singh, T P]]
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[[Category: Sinha, M.]]
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[[Category: Sinha, M]]
[[Category: Antibiotic]]
[[Category: Antibiotic]]
[[Category: Antimicrobial]]
[[Category: Antimicrobial]]

Revision as of 16:15, 18 December 2014

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with N-acetyl glucosamine(NAG) at 2.6 A resolution

3nkw, resolution 2.60Å

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