4zxm - Revision history

OCA at 15:47, 8 November 2023

OCA — Wed, 08 Nov 2023 15:47:44 GMT

←Older revision		Revision as of 15:47, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Branchiostoma_belcheri_tsingtauense Branchiostoma belcheri tsingtauense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZXM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Branchiostoma_belcheri_tsingtauense Branchiostoma belcheri tsingtauense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZXM 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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [https://pdbe.org/4zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [https://www.ebi.ac.uk/pdbsum/4zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zxm ProSAT]</span></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]] 2.8Å</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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [https://pdbe.org/4zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [https://www.ebi.ac.uk/pdbsum/4zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zxm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:45, 18 May 2023

OCA — Thu, 18 May 2023 07:45:48 GMT

←Older revision		Revision as of 07:45, 18 May 2023
Line 3:		Line 3:
	<StructureSection load='4zxm' size='340' side='right'caption='[[4zxm]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='4zxm' size='340' side='right'caption='[[4zxm]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachiostoma_belcheri_tsingtauense Brachiostoma~~ belcheri tsingtauense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Branchiostoma_belcheri_tsingtauense Branchiostoma belcheri tsingtauense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZXM FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [https://pdbe.org/4zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [https://www.ebi.ac.uk/pdbsum/4zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zxm 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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [~~http~~://pdbe.org/4zxm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zxm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zxm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0R4I988_BRABE A0A0R4I988_BRABE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachiostoma~~ belcheri tsingtauense]]	+	[[Category: Branchiostoma belcheri tsingtauense]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylmuramoyl-L-alanine amidase]]~~	+	[[Category: Cheng W]]
-	[[Category: Cheng, W]]	+	[[Category: Jiang YL]]
-	[[Category: Jiang~~, Y L~~]]	+	[[Category: Luo M]]
-	[[Category: Luo, M]]	+	[[Category: Wang WJ]]
-	[[Category: Wang~~, W J~~]]	+	[[Category: Yu HM]]
-	[[Category: Yu~~, H M]]~~	+
-	~~[[Category: Amidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidoglycan recognition protein~~]]	+

OCA at 08:05, 26 June 2019

OCA — Wed, 26 Jun 2019 08:05:21 GMT

←Older revision		Revision as of 08:05, 26 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3==		==Crystal structure of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3==
-	<StructureSection load='4zxm' size='340' side='right' caption='[[4zxm]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='4zxm' size='340' side='right'caption='[[4zxm]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachiostoma_belcheri_tsingtauense Brachiostoma belcheri tsingtauense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZXM FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [http://pdbe.org/4zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [http://www.ebi.ac.uk/pdbsum/4zxm 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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [http://pdbe.org/4zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [http://www.ebi.ac.uk/pdbsum/4zxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zxm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachiostoma belcheri tsingtauense]]
		+	[[Category: Large Structures]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
	[[Category: Cheng, W]]		[[Category: Cheng, W]]

OCA at 19:16, 30 November 2015

OCA — Mon, 30 Nov 2015 19:16:32 GMT

←Older revision		Revision as of 19:16, 30 November 2015
Line 6:		Line 6:
	<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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [http://pdbe.org/4zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [http://www.ebi.ac.uk/pdbsum/4zxm 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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [http://pdbe.org/4zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [http://www.ebi.ac.uk/pdbsum/4zxm PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 A crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum.
		+
		+	Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain.,Wang WJ, Cheng W, Luo M, Yan Q, Yu HM, Li Q, Cao DD, Huang S, Xu A, Mariuzza RA, Chen Y, Zhou CZ PLoS One. 2015 Oct 19;10(10):e0140953. doi: 10.1371/journal.pone.0140953., eCollection 2015. PMID:26479246<ref>PMID:26479246</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4zxm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:05, 16 October 2015

OCA — Fri, 16 Oct 2015 04:05:52 GMT

←Older revision		Revision as of 04:05, 16 October 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3==
-		+	<StructureSection load='4zxm' size='340' side='right' caption='[[4zxm]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~The entry~~ 4zxm is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4zxm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZXM FirstGlance]. <br>
-	~~Authors~~: ~~Wang, W~~.J.~~, Cheng, W~~.~~, Jiang, Y~~.L.~~, Yu, H~~.M.~~, Luo, M~~.	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=4zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zxm OCA], [http://pdbe.org/4zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zxm RCSB], [http://www.ebi.ac.uk/pdbsum/4zxm PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal structure of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	__TOC__
-	[~~[Category~~: ~~Luo, M~~]]	+	</StructureSection>
-	[[~~Category~~: ~~Wang~~, W.J]]	+	[[Category: N-acetylmuramoyl-L-alanine amidase]]
-	[~~[Category~~: Yu, H.M]]	+
-	[[Category: ~~Jiang, Y.~~L]]	+
	[[Category: Cheng, W]]		[[Category: Cheng, W]]
		+	[[Category: Jiang, Y L]]
		+	[[Category: Luo, M]]
		+	[[Category: Wang, W J]]
		+	[[Category: Yu, H M]]
		+	[[Category: Amidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidoglycan recognition protein]]

OCA at 12:25, 10 June 2015

OCA — Wed, 10 Jun 2015 12:25:02 GMT

←Older revision		Revision as of 12:25, 10 June 2015
Line 5:		Line 5:
	Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M.		Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M.

-	Description: Crystal ~~stucture~~ of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3	+	Description: Crystal structure of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Luo, M]]		[[Category: Luo, M]]

OCA at 11:18, 3 June 2015

OCA — Wed, 03 Jun 2015 11:18:11 GMT

←Older revision		Revision as of 11:18, 3 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4zxm is ON HOLD	+	The entry 4zxm is ON HOLD until Paper Publication

	Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M.		Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M.

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

OCA — Wed, 27 May 2015 14:52:33 GMT

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

←Older revision

Revision as of 14:52, 27 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zxm is ON HOLD Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M. Description: Crystal stucture of PGRP domain from Branchiostoma belc...

OCA — Wed, 27 May 2015 14:52:32 GMT

New page: '''Unreleased structure''' The entry 4zxm is ON HOLD Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M. Description: Crystal stucture of PGRP domain from Branchiostoma belc...

New page

'''Unreleased structure'''

The entry 4zxm is ON HOLD

Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Yu, H.M., Luo, M.

Description: Crystal stucture of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3
[[Category: Unreleased Structures]]
[[Category: Luo, M]]
[[Category: Wang, W.J]]
[[Category: Yu, H.M]]
[[Category: Jiang, Y.L]]
[[Category: Cheng, W]]