2erv

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the outer membrane enzyme PagL

Structural highlights

2erv is a 2 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PAGL_PSEAE Has lipid A 3-O-deacylase activity. Hydrolyzes the ester bond at the 3 position of lipid A, a bioactive component of lipopolysaccharide (LPS), thereby releasing the primary fatty acyl moiety. Lacks fatty acyl chain-length specificity as removes both 3-OH C10 and 3-OH C14 fatty acids from lipid A.^[1] ^[2] ^[3]

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

Pathogenic gram-negative bacteria can modify the lipid A portion of their lipopolysaccharide in response to environmental stimuli. 3-O-deacylation of lipid A by the outer membrane enzyme PagL modulates signaling through Toll-like receptor 4, leading to a reduced host immune response. We found that PagL is widely disseminated among gram-negative bacteria. Only four residues are conserved: a Ser, His, Phe, and Asn residue. Here, we describe the crystal structure of PagL from Pseudomonas aeruginosa to 2.0-A resolution. It consists of an eight-stranded beta-barrel with the axis tilted by approximately 30 degrees with respect to the lipid bilayer. The structure reveals that PagL contains an active site with a Ser-His-Glu catalytic triad and an oxyanion hole that comprises the conserved Asn. The importance of active site residues was confirmed in mutagenesis studies. Although PagL is most likely active as a monomer, its active site architecture shows high resemblance to that of the dimeric 12-stranded outer membrane phospholipase A. Modeling of the substrate lipid X onto the active site reveals that the 3-O-acyl chain is accommodated in a hydrophobic groove perpendicular to the membrane plane. In addition, an aspartate makes a hydrogen bond with the hydroxyl group of the 3-O-acyl chain, probably providing specificity of PagL toward lipid A.

Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa.,Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, Tommassen J Proc Natl Acad Sci U S A. 2006 May 2;103(18):7071-6. Epub 2006 Apr 21. PMID:16632613^[4]

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

References

↑ Geurtsen J, Steeghs L, Hove JT, van der Ley P, Tommassen J. Dissemination of lipid A deacylases (pagL) among gram-negative bacteria: identification of active-site histidine and serine residues. J Biol Chem. 2005 Mar 4;280(9):8248-59. Epub 2004 Dec 20. PMID:15611102 doi:http://dx.doi.org/10.1074/jbc.M414235200
↑ Ernst RK, Adams KN, Moskowitz SM, Kraig GM, Kawasaki K, Stead CM, Trent MS, Miller SI. The Pseudomonas aeruginosa lipid A deacylase: selection for expression and loss within the cystic fibrosis airway. J Bacteriol. 2006 Jan;188(1):191-201. PMID:16352835 doi:http://dx.doi.org/10.1128/JB.188.1.191-201.2006
↑ Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, Tommassen J. Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2006 May 2;103(18):7071-6. Epub 2006 Apr 21. PMID:16632613
↑ Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, Tommassen J. Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2006 May 2;103(18):7071-6. Epub 2006 Apr 21. PMID:16632613

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/2erv"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the outer membrane enzyme PagL==
-<StructureSection load='2erv' size='340' side='right' caption='[[2erv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='2erv' size='340' side='right'caption='[[2erv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2erv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ERV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ERV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2erv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ERV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ERV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CXE:PENTAETHYLENE+GLYCOL+MONODECYL+ETHER'>CXE</scene></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]] 2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA4661 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CXE:PENTAETHYLENE+GLYCOL+MONODECYL+ETHER'>CXE</scene></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=2erv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2erv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2erv RCSB], [http://www.ebi.ac.uk/pdbsum/2erv 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=2erv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2erv OCA], [https://pdbe.org/2erv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2erv RCSB], [https://www.ebi.ac.uk/pdbsum/2erv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2erv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q9HVD1_PSEAE Q9HVD1_PSEAE]] Has lipid A 3-O-deacylase activity. Hydrolyzes the ester bond at the 3 position of lipid A, a bioactive component of lipopolysaccharide (LPS), thereby releasing the primary fatty acyl moiety. Lacks fatty acyl chain-length specificity as removes both 3-OH C10 and 3-OH C14 fatty acids from lipid A.<ref>PMID:15611102</ref> <ref>PMID:16352835</ref> <ref>PMID:16632613</ref>
+[https://www.uniprot.org/uniprot/PAGL_PSEAE PAGL_PSEAE] Has lipid A 3-O-deacylase activity. Hydrolyzes the ester bond at the 3 position of lipid A, a bioactive component of lipopolysaccharide (LPS), thereby releasing the primary fatty acyl moiety. Lacks fatty acyl chain-length specificity as removes both 3-OH C10 and 3-OH C14 fatty acids from lipid A.<ref>PMID:15611102</ref> <ref>PMID:16352835</ref> <ref>PMID:16632613</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/er/2erv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/2erv_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=2erv ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2erv" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Bonvin, A M]]
+[[Category: Bonvin AM]]
-[[Category: Egmond, M R]]
+[[Category: Egmond MR]]
-[[Category: Geurtsen, J]]
+[[Category: Geurtsen J]]
-[[Category: Gros, P]]
+[[Category: Gros P]]
-[[Category: Lambert, W]]
+[[Category: Lambert W]]
-[[Category: Ley, P van der]]
+[[Category: Rutten L]]
-[[Category: Rutten, L]]
+[[Category: Smolenaers JJ]]
-[[Category: Smolenaers, J J]]
+[[Category: Tommassen J]]
-[[Category: Tommassen, J]]
+[[Category: Van der Ley P]]
-[[Category: Beta barrel]]
-[[Category: Enzyme]]
-[[Category: Hydrolase]]
-[[Category: Lipopolysaccharide]]
-[[Category: Membrane protein]]
-[[Category: Outer membrane]]

2erv

From Proteopedia

Current revision

Crystal structure of the outer membrane enzyme PagL

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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