4z8i - Revision history

OCA at 15:42, 8 November 2023

OCA — Wed, 08 Nov 2023 15:42:35 GMT

←Older revision		Revision as of 15:42, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4z8i]] 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=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>		<table><tr><td colspan='2'>[[4z8i]] 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=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.701Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [https://pdbe.org/4z8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [https://www.ebi.ac.uk/pdbsum/4z8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8i ProSAT]</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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [https://pdbe.org/4z8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [https://www.ebi.ac.uk/pdbsum/4z8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8i ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:43, 10 May 2023

OCA — Wed, 10 May 2023 07:43:31 GMT

←Older revision		Revision as of 07:43, 10 May 2023
Line 3:		Line 3:
	<StructureSection load='4z8i' size='340' side='right'caption='[[4z8i]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4z8i' size='340' side='right'caption='[[4z8i]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4z8i]] 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=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4z8i]] 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=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [https://pdbe.org/4z8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [https://www.ebi.ac.uk/pdbsum/4z8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8i 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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [~~http~~://pdbe.org/4z8i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4z8i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0R4I979_BRABE A0A0R4I979_BRABE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__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: Cao DD]]
-	[[Category: Cao~~, D D~~]]	+	[[Category: Chen Y]]
-	[[Category: Chen, Y]]	+	[[Category: Cheng W]]
-	[[Category: Cheng, W]]	+	[[Category: Chi CB]]
-	[[Category: Chi~~, C B~~]]	+	[[Category: Jiang YL]]
-	[[Category: Jiang~~, Y L~~]]	+	[[Category: Luo M]]
-	[[Category: Luo, M]]	+	[[Category: Wang WJ]]
-	[[Category: Wang~~, W J~~]]	+	[[Category: Yang HB]]
-	[[Category: Yang~~, H B~~]]	+	[[Category: Zhou CZ]]
-	[[Category: Zhou~~, C Z]]~~	+
-	~~[[Category: Amidase]]~~	+
-	~~[[Category: Chitin-binding domain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidoglycan recognition protein~~]]	+

OCA at 07:37, 19 June 2019

OCA — Wed, 19 Jun 2019 07:37:53 GMT

←Older revision		Revision as of 07:37, 19 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3==		==Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3==
-	<StructureSection load='4z8i' size='340' side='right' caption='[[4z8i]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4z8i' size='340' side='right'caption='[[4z8i]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4z8i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4z8i]] 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=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [http://pdbe.org/4z8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [http://www.ebi.ac.uk/pdbsum/4z8i 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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [http://pdbe.org/4z8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [http://www.ebi.ac.uk/pdbsum/4z8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachiostoma belcheri tsingtauense]]
		+	[[Category: Large Structures]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
	[[Category: Cao, D D]]		[[Category: Cao, D D]]

OCA at 22:10, 30 November 2015

OCA — Mon, 30 Nov 2015 22:10:25 GMT

←Older revision		Revision as of 22:10, 30 November 2015
Line 7:		Line 7:
	<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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [http://pdbe.org/4z8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [http://www.ebi.ac.uk/pdbsum/4z8i 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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [http://pdbe.org/4z8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [http://www.ebi.ac.uk/pdbsum/4z8i 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 4z8i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:05, 16 October 2015

OCA — Fri, 16 Oct 2015 04:05:01 GMT

←Older revision		Revision as of 04:05, 16 October 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3==
-		+	<StructureSection load='4z8i' size='340' side='right' caption='[[4z8i]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~The entry~~ 4z8i is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4z8i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8I FirstGlance]. <br>
-	~~Authors~~: ~~Wang, W~~.J.~~, Cheng, W~~.~~, Jiang, Y~~.L.~~, Luo, M~~.~~, Cao, D~~.D.~~, Chi, C~~.B., ~~Yang, H~~.B.~~, Chen, Y~~.~~, Zhou, C~~.Z.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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>
-	~~Description: Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein~~ 3	+	<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=4z8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8i OCA], [http://pdbe.org/4z8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8i RCSB], [http://www.ebi.ac.uk/pdbsum/4z8i PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures]~~]	+	</table>
-	[[~~Category~~: ~~Cao~~, D.D]]	+	__TOC__
-	[[Category: ~~Yang, H.B~~]]	+	</StructureSection>
-	[[Category: ~~Luo~~, M]]	+	[[Category: N-acetylmuramoyl-L-alanine amidase]]
		+	[[Category: Cao, D D]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
-	[[Category: Wang, W.J]]
-	[[Category: Zhou, C.Z]]
-	[[Category: Chi, C.B]]
-	[[Category: Jiang, Y.L]]
	[[Category: Cheng, W]]		[[Category: Cheng, W]]
		+	[[Category: Chi, C B]]
		+	[[Category: Jiang, Y L]]
		+	[[Category: Luo, M]]
		+	[[Category: Wang, W J]]
		+	[[Category: Yang, H B]]
		+	[[Category: Zhou, C Z]]
		+	[[Category: Amidase]]
		+	[[Category: Chitin-binding domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidoglycan recognition protein]]

OCA at 14:09, 27 May 2015

OCA — Wed, 27 May 2015 14:09:42 GMT

←Older revision		Revision as of 14:09, 27 May 2015
Line 5:		Line 5:
	Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z.		Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z.

-	Description: Crystal ~~stucture of~~ of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 1	+	Description: Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Cao, D.D]]		[[Category: Cao, D.D]]

OCA at 11:33, 22 April 2015

OCA — Wed, 22 Apr 2015 11:33:19 GMT

←Older revision		Revision as of 11:33, 22 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4z8i is ON HOLD	+	The entry 4z8i is ON HOLD until Paper Publication

	Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z.		Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z.

OCA: Protected "4z8i" [edit=sysop:move=sysop]

OCA — Wed, 15 Apr 2015 11:48:38 GMT

Protected "4z8i" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:48, 15 April 2015

OCA: New page: '''Unreleased structure''' The entry 4z8i is ON HOLD Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z. Description: Crystal s...

OCA — Wed, 15 Apr 2015 11:48:37 GMT

New page: '''Unreleased structure''' The entry 4z8i is ON HOLD Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z. Description: Crystal s...

New page

'''Unreleased structure'''

The entry 4z8i is ON HOLD

Authors: Wang, W.J., Cheng, W., Jiang, Y.L., Luo, M., Cao, D.D., Chi, C.B., Yang, H.B., Chen, Y., Zhou, C.Z.

Description: Crystal stucture of of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 1
[[Category: Unreleased Structures]]
[[Category: Cao, D.D]]
[[Category: Yang, H.B]]
[[Category: Luo, M]]
[[Category: Chen, Y]]
[[Category: Wang, W.J]]
[[Category: Zhou, C.Z]]
[[Category: Chi, C.B]]
[[Category: Jiang, Y.L]]
[[Category: Cheng, W]]