2aiz - Revision history

OCA at 10:31, 15 February 2023

2023-02-15T10:31:09Z

←Older revision		Revision as of 10:31, 15 February 2023
Line 1:		Line 1:

-	====	+	==Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine==
	<StructureSection load='2aiz' size='340' side='right'caption='[[2aiz]]' scene=''>		<StructureSection load='2aiz' size='340' side='right'caption='[[2aiz]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2aiz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AIZ FirstGlance]. <br>
-	</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [https://pdbe.org/2aiz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [https://www.ebi.ac.uk/pdbsum/2aiz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aiz ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=AMU:BETA-N-ACETYLMURAMIC+ACID'>AMU</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [https://pdbe.org/2aiz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [https://www.ebi.ac.uk/pdbsum/2aiz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aiz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PAL_HAEIN PAL_HAEIN] Thought to play a role in bacterial envelope integrity. Links the outer membrane to the peptidoglycan layer.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 19:
	</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=2aiz 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=2aiz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan-associated lipoprotein (Pal) is a potential vaccine candidate from Haemophilus influenzae that is highly conserved in Gram-negative bacteria and anchored to the outer membrane through an N-terminal lipid attachment. Pal stabilizes the outer membrane by providing a noncovalent link to the peptidoglycan (PG) layer through a periplasmic domain. Using NMR spectroscopy, we determined the three-dimensional structure of a complex between the periplasmic domain of Pal and a biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-alpha-d-Glu-m-Dap-D-Ala-d-Ala (m-Dap is meso-diaminopimelate). Pal has a binding pocket lined with conserved surface residues that interacts exclusively with the peptide portion of the ligand. The m-Dap residue, which is mainly found in the cell walls of Gram-negative bacteria, is sequestered in this pocket and plays an important role by forming hydrogen bond and hydrophobic contacts to Pal. The structure provides insight into the mode of cell wall recognition for a broad class of Gram-negative membrane proteins, including OmpA and MotB, which have peptidoglycan-binding domains homologous to that of Pal.
		+
		+	Peptidoglycan recognition by Pal, an outer membrane lipoprotein.,Parsons LM, Lin F, Orban J Biochemistry. 2006 Feb 21;45(7):2122-8. PMID:16475801<ref>PMID:16475801</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 2aiz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Haemophilus influenzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Lin F]]
		+	[[Category: Orban J]]
		+	[[Category: Parsons LM]]

OCA at 11:31, 3 February 2021

2021-02-03T11:31:47Z

←Older revision		Revision as of 11:31, 3 February 2021
Line 1:		Line 1:

-	==~~Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine~~==	+	====
-	<StructureSection load='2aiz' size='340' side='right' caption='[[2aiz~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2aiz' size='340' side='right'caption='[[2aiz]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896].~~ Full ~~experimental~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=~~2AIZ~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=~~2AIZ~~ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= 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></td></tr>~~	+	</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [https://pdbe.org/2aiz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [https://www.ebi.ac.uk/pdbsum/2aiz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aiz ProSAT]</span></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [~~http~~://pdbe.org/2aiz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2aiz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2aiz ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/PAL_HAEIN PAL_HAEIN]] Thought to play a role in bacterial envelope integrity. Links the outer membrane to the peptidoglycan layer.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 16:
	</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=2aiz 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=2aiz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Peptidoglycan-associated lipoprotein (Pal) is a potential vaccine candidate from Haemophilus influenzae that is highly conserved in Gram-negative bacteria and anchored to the outer membrane through an N-terminal lipid attachment. Pal stabilizes the outer membrane by providing a noncovalent link to the peptidoglycan (PG) layer through a periplasmic domain. Using NMR spectroscopy, we determined the three-dimensional structure of a complex between the periplasmic domain of Pal and a biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-alpha-d-Glu-m-Dap-D-Ala-d-Ala (m-Dap is meso-diaminopimelate). Pal has a binding pocket lined with conserved surface residues that interacts exclusively with the peptide portion of the ligand. The m-Dap residue, which is mainly found in the cell walls of Gram-negative bacteria, is sequestered in this pocket and plays an important role by forming hydrogen bond and hydrophobic contacts to Pal. The structure provides insight into the mode of cell wall recognition for a broad class of Gram-negative membrane proteins, including OmpA and MotB, which have peptidoglycan-binding domains homologous to that of Pal.
-
-	Peptidoglycan recognition by Pal, an outer membrane lipoprotein.,Parsons LM, Lin F, Orban J Biochemistry. 2006 Feb 21;45(7):2122-8. PMID:16475801<ref>PMID:16475801</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2aiz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium influenzae lehmann and neumann 1896~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lin, F]]~~	+	[[Category: Z-disk]]
-	~~[[Category: Orban, J]]~~	+
-	~~[[Category: Parsons, L M]]~~	+
-	~~[[Category: S2F, Structure 2.Function Project]]~~	+
-	~~[[Category: Alpha~~-~~beta sandwich]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: S2f]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Structure 2 function project~~]]	+

OCA at 06:50, 9 May 2018

2018-05-09T06:50:51Z

←Older revision		Revision as of 06:50, 9 May 2018
Line 1:		Line 1:
		+
	==Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine==		==Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine==
	<StructureSection load='2aiz' size='340' side='right' caption='[[2aiz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2aiz' size='340' side='right' caption='[[2aiz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://pdbe.org/2aiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz 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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://pdbe.org/2aiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2aiz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ai/2aiz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ai/2aiz_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 16:20, 7 February 2016

2016-02-07T16:20:04Z

←Older revision		Revision as of 16:20, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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=2aiz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:10, 10 September 2015

2015-09-10T03:10:55Z

←Older revision		Revision as of 03:10, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2aiz' size='340' side='right' caption='[[2aiz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2aiz' size='340' side='right' caption='[[2aiz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Haemophilus_influenzae Haemophilus~~ influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AIZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AIZ 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></td></tr>		</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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 ~~Haemophilus~~ influenzae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz 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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://pdbe.org/2aiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2aiz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haemophilus~~ influenzae]]	+	[[Category: Bacterium influenzae lehmann and neumann 1896]]
	[[Category: Lin, F]]		[[Category: Lin, F]]
	[[Category: Orban, J]]		[[Category: Orban, J]]

OCA at 16:38, 24 December 2014

2014-12-24T16:38:29Z

←Older revision		Revision as of 16:38, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AIZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AIZ 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><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz 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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAL_HAEIN PAL_HAEIN]] Thought to play a role in bacterial envelope integrity. Links the outer membrane to the peptidoglycan layer.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
-	[[Category: Lin, F.]]	+	[[Category: Lin, F]]
-	[[Category: Orban, J.]]	+	[[Category: Orban, J]]
-	[[Category: Parsons, L M.]]	+	[[Category: Parsons, L M]]
-	[[Category: S2F, Structure 2.Function Project.]]	+	[[Category: S2F, Structure 2.Function Project]]
	[[Category: Alpha-beta sandwich]]		[[Category: Alpha-beta sandwich]]
	[[Category: Membrane protein]]		[[Category: Membrane protein]]

OCA at 02:26, 30 September 2014

2014-09-30T02:26:08Z

←Older revision		Revision as of 02:26, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2aiz.~~png~~\|~~left~~\|200px]]	+	==Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine==
		+	<StructureSection load='2aiz' size='340' side='right' caption='[[2aiz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AIZ 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><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6CL:6-CARBOXYLYSINE'>6CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pal, ompP6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</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=2aiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aiz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aiz RCSB], [http://www.ebi.ac.uk/pdbsum/2aiz PDBsum]</span></td></tr>
		+	<table>
		+	== 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/ai/2aiz_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].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan-associated lipoprotein (Pal) is a potential vaccine candidate from Haemophilus influenzae that is highly conserved in Gram-negative bacteria and anchored to the outer membrane through an N-terminal lipid attachment. Pal stabilizes the outer membrane by providing a noncovalent link to the peptidoglycan (PG) layer through a periplasmic domain. Using NMR spectroscopy, we determined the three-dimensional structure of a complex between the periplasmic domain of Pal and a biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-alpha-d-Glu-m-Dap-D-Ala-d-Ala (m-Dap is meso-diaminopimelate). Pal has a binding pocket lined with conserved surface residues that interacts exclusively with the peptide portion of the ligand. The m-Dap residue, which is mainly found in the cell walls of Gram-negative bacteria, is sequestered in this pocket and plays an important role by forming hydrogen bond and hydrophobic contacts to Pal. The structure provides insight into the mode of cell wall recognition for a broad class of Gram-negative membrane proteins, including OmpA and MotB, which have peptidoglycan-binding domains homologous to that of Pal.

-	~~{{STRUCTURE_2aiz\| PDB=2aiz \| SCENE= }}~~	+	Peptidoglycan recognition by Pal, an outer membrane lipoprotein.,Parsons LM, Lin F, Orban J Biochemistry. 2006 Feb 21;45(7):2122-8. PMID:16475801<ref>PMID:16475801</ref>

-	~~===Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2~~,~~6-diaminopimeloyl-D-alanyl-D-alanine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16475801}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2aiz]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Haemophilus_influenzae Haemophilus influenzae]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016475801<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: Lin, F.]]		[[Category: Lin, F.]]

OCA: Protected "2aiz" [edit=sysop:move=sysop]

2013-01-06T11:38:38Z

Protected "2aiz" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:38, 6 January 2013

OCA at 11:38, 6 January 2013

2013-01-06T11:38:35Z

←Older revision		Revision as of 11:38, 6 January 2013
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-	{{Seed}}
	[[Image:2aiz.png\|left\|200px]]		[[Image:2aiz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2aiz", 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.
-	-->
	{{STRUCTURE_2aiz\| PDB=2aiz \| SCENE= }}		{{STRUCTURE_2aiz\| PDB=2aiz \| SCENE= }}

	===Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine===		===Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16475801}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16475801 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16475801}}		{{ABSTRACT_PUBMED_16475801}}

	==About this Structure==		==About this Structure==
-	~~2AIZ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA].	+	[[2aiz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16475801~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016475801</ref><references group="xtra"/>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: Lin, F.]]		[[Category: Lin, F.]]
Line 30:		Line 18:
	[[Category: S2F, Structure 2.Function Project.]]		[[Category: S2F, Structure 2.Function Project.]]
	[[Category: Alpha-beta sandwich]]		[[Category: Alpha-beta sandwich]]
		+	[[Category: Membrane protein]]
	[[Category: S2f]]		[[Category: S2f]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structure 2 function project]]		[[Category: Structure 2 function project]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:03:52 2009''

OCA at 13:03, 16 February 2009

2009-02-16T13:03:53Z

←Older revision		Revision as of 13:03, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2AIZ is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA].	+	2AIZ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIZ OCA].

	==Reference==		==Reference==
-	~~Peptidoglycan recognition by Pal, an outer membrane lipoprotein., Parsons LM, Lin F, Orban J, Biochemistry. 2006 Feb 21;45(7):2122-8.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16475801 16475801]~~	+	<ref group="xtra">PMID:16475801</ref><references group="xtra"/>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
-	[[Category: Single protein]]
	[[Category: Lin, F.]]		[[Category: Lin, F.]]
	[[Category: Orban, J.]]		[[Category: Orban, J.]]
Line 35:		Line 34:
	[[Category: Structure 2 function project]]		[[Category: Structure 2 function project]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 17~~:51:52 ~~2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:03:52 2009''