4h4j - Revision history

OCA at 07:58, 3 November 2022

2022-11-03T07:58:50Z

←Older revision		Revision as of 07:58, 3 November 2022
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	==Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution==		==Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution==
-	<StructureSection load='4h4j' size='340' side='right' caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>	+	<StructureSection load='4h4j' size='340' side='right'caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h4j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacuc Bacuc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h4j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_uniformis_ATCC_8492 Bacteroides uniformis ATCC 8492]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H4J FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACUNI_02947, ZP_02071508.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411479 BACUC])</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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [https://pdbe.org/4h4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [https://www.ebi.ac.uk/pdbsum/4h4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h4j ProSAT]</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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [~~http~~://pdbe.org/4h4j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h4j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h4j ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A7V5T8_BACUC A7V5T8_BACUC]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 A resolution shows that AmiA is related to NlpC/P60 gamma-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family.
		+
		+	Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.,Xu Q, Mengin-Lecreulx D, Patin D, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA Structure. 2014 Dec 2;22(12):1799-1809. doi: 10.1016/j.str.2014.09.018. Epub 2014, Nov 20. PMID:25465128<ref>PMID:25465128</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4h4j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacuc~~]]	+	[[Category: Bacteroides uniformis ATCC 8492]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Duf 1460]]~~	+
-	~~[[Category: Jcsg]]~~	+
-	~~[[Category: Pf07313 family protein]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 08:35, 15 November 2017

2017-11-15T08:35:49Z

←Older revision		Revision as of 08:35, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='4h4j' size='340' side='right' caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='4h4j' size='340' side='right' caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteroides_uniformis_atcc_8492 Bacteroides uniformis atcc 8492~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacuc Bacuc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H4J FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACUNI_02947, ZP_02071508.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411479 ~~Bacteroides uniformis ATCC 8492~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACUNI_02947, ZP_02071508.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411479 BACUC])</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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [http://pdbe.org/4h4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [http://www.ebi.ac.uk/pdbsum/4h4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h4j ProSAT]</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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [http://pdbe.org/4h4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [http://www.ebi.ac.uk/pdbsum/4h4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h4j ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteroides uniformis atcc 8492~~]]	+	[[Category: Bacuc]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Duf 1460]]		[[Category: Duf 1460]]

OCA at 04:45, 5 August 2016

2016-08-05T04:45:41Z

←Older revision		Revision as of 04:45, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution==		==Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution==
	<StructureSection load='4h4j' size='340' side='right' caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='4h4j' size='340' side='right' caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACUNI_02947, ZP_02071508.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411479 Bacteroides uniformis ATCC 8492])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACUNI_02947, ZP_02071508.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411479 Bacteroides uniformis ATCC 8492])</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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [http://www.ebi.ac.uk/pdbsum/4h4j 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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [http://pdbe.org/4h4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [http://www.ebi.ac.uk/pdbsum/4h4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h4j ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 11:21, 24 December 2014

2014-12-24T11:21:27Z

←Older revision		Revision as of 11:21, 24 December 2014
Line 1:		Line 1:
-	~~[[Image:4h4j.jpg\|left\|200px]]~~	+	==Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution==
-		+	<StructureSection load='4h4j' size='340' side='right' caption='[[4h4j]], [[Resolution\|resolution]] 1.15Å' scene=''>
-	~~{{STRUCTURE_4h4j\| PDB=4h4j \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4h4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_uniformis_atcc_8492 Bacteroides uniformis atcc 8492]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H4J FirstGlance]. <br>
-	===Crystal structure of a ~~hypothetical protein~~ (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution===	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACUNI_02947, ZP_02071508.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411479 Bacteroides uniformis ATCC 8492])</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=4h4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h4j RCSB], [http://www.ebi.ac.uk/pdbsum/4h4j PDBsum]</span></td></tr>
-	==~~About this Structure~~==	+	</table>
-	[[4h4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_uniformis_atcc_8492 Bacteroides uniformis atcc 8492]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA].	+	__TOC__
		+	</StructureSection>
	[[Category: Bacteroides uniformis atcc 8492]]		[[Category: Bacteroides uniformis atcc 8492]]
-	[[Category: ~~JCSG, Joint Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
	[[Category: Duf 1460]]		[[Category: Duf 1460]]
	[[Category: Jcsg]]		[[Category: Jcsg]]
-	[[Category: Joint center for structural genomic]]
	[[Category: Pf07313 family protein]]		[[Category: Pf07313 family protein]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics unknown function]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 07:15, 17 October 2012

2012-10-17T07:15:59Z

←Older revision		Revision as of 07:15, 17 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4h4j.jpg\|left\|200px]]

-	~~The entry~~ 4h4j ~~is ON HOLD~~	+	{{STRUCTURE_4h4j\| PDB=4h4j \| SCENE= }}

-	~~Authors: Joint Center for Structural Genomics~~ (~~JCSG~~)	+	===Crystal structure of a hypothetical protein (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution===

-	~~Description: Crystal structure of~~ a ~~hypothetical protein (BACUNI_02947)~~ from Bacteroides uniformis ~~ATCC~~ 8492 ~~at 1~~.~~15 A resolution~~	+
		+	==About this Structure==
		+	[[4h4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_uniformis_atcc_8492 Bacteroides uniformis atcc 8492]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4J OCA].
		+	[[Category: Bacteroides uniformis atcc 8492]]
		+	[[Category: JCSG, Joint Center for Structural Genomics.]]
		+	[[Category: Duf 1460]]
		+	[[Category: Jcsg]]
		+	[[Category: Joint center for structural genomic]]
		+	[[Category: Pf07313 family protein]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-biology]]
		+	[[Category: Structural genomic]]
		+	[[Category: Structural genomics unknown function]]
		+	[[Category: Unknown function]]

OCA: Protected "4h4j" [edit=sysop:move=sysop]

2012-09-26T20:12:15Z

Protected "4h4j" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:12, 26 September 2012

OCA: New page: '''Unreleased structure''' The entry 4h4j is ON HOLD Authors: Joint Center for Structural Genomics (JCSG) Description: Crystal structure of a hypothetical protein (BACUNI_02947) from B...

2012-09-26T20:12:14Z

New page: '''Unreleased structure''' The entry 4h4j is ON HOLD Authors: Joint Center for Structural Genomics (JCSG) Description: Crystal structure of a hypothetical protein (BACUNI_02947) from B...

New page

'''Unreleased structure'''

The entry 4h4j is ON HOLD

Authors: Joint Center for Structural Genomics (JCSG)

Description: Crystal structure of a hypothetical protein (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution