6agq - Revision history

OCA at 10:31, 27 March 2024

OCA — Wed, 27 Mar 2024 10:31:46 GMT

←Older revision		Revision as of 10:31, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6agq' size='340' side='right'caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6agq' size='340' side='right'caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Paenibacillus_sp.~~_r4~~ Paenibacillus sp. r4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6AGQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_sp._R4 Paenibacillus sp. R4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AGQ 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]] 2.1Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [~~http~~://pdbe.org/6agq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6agq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq ProSAT]</span></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=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [https://pdbe.org/6agq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [https://www.ebi.ac.uk/pdbsum/6agq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A452CSP2_9BACL A0A452CSP2_9BACL]
-	Cold-active acetyl xylan esterases allow for reduced bioreactor heating costs in bioenergy production. Here, we isolated and characterized a cold-active acetyl xylan esterase (PbAcE) from the psychrophilic soil microbe Paenibacillus sp. R4. The enzyme hydrolyzes glucose penta-acetate and xylan acetate, reversibly producing acetyl xylan from xylan, and it shows higher activity at 4 degrees C than at 25 degrees C. We solved the crystal structure of PbAcE at 2.1-A resolution to investigate its active site and the reason for its low-temperature activity. Structural analysis showed that PbAcE forms a hexamer with a central substrate binding tunnel, and the inter-subunit interactions are relatively weak compared with those of its mesophilic and thermophilic homologs. PbAcE also has a shorter loop and different residue composition in the beta4-alpha3 and beta5-alpha4 regions near the substrate binding site. Flexible subunit movements and different active site loop conformations may enable the strong low-temperature activity and broad substrate specificity of PbAcE. In addition, PbAcE was found to have strong activity against antibiotic compound substrates, such as cefotaxime and 7-amino cephalosporanic acid (7-ACA). In conclusion, the PbAcE structure and our biochemical results provide the first example of a cold-active acetyl xylan esterase and a starting template for structure-based protein engineering.	+
-		+
-	Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp.,Park SH, Yoo W, Lee CW, Jeong CS, Shin SC, Kim HW, Park H, Kim KK, Kim TD, Lee JH PLoS One. 2018 Oct 31;13(10):~~e0206260. doi: 10.1371~~/~~journal.pone.0206260., eCollection 2018. PMID:30379876<ref>PMID:30379876<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6agq" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Paenibacillus sp. r4]]	+	[[Category: Paenibacillus sp. R4]]
-	[[Category: Lee~~, C W~~]]	+	[[Category: Lee CW]]
-	[[Category: Lee~~, J H~~]]	+	[[Category: Lee JH]]
-	[[Category: Park, S]]	+	[[Category: Park S]]
-	~~[[Category: Acetyl esterase]]~~	+
-	~~[[Category: Acetyl xylan esterase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Paenibacillus sp~~]]	+

OCA at 21:27, 28 October 2020

OCA — Wed, 28 Oct 2020 21:27:58 GMT

←Older revision		Revision as of 21:27, 28 October 2020
Line 1:		Line 1:

	==Acetyl xylan esterase from Paenibacillus sp. R4==		==Acetyl xylan esterase from Paenibacillus sp. R4==
-	<StructureSection load='6agq' size='340' side='right' caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='6agq' size='340' side='right'caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_sp._r4 Paenibacillus sp. r4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AGQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_sp._r4 Paenibacillus sp. r4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AGQ 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='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=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [http://pdbe.org/6agq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [http://www.ebi.ac.uk/pdbsum/6agq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [http://pdbe.org/6agq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [http://www.ebi.ac.uk/pdbsum/6agq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Paenibacillus sp. r4]]		[[Category: Paenibacillus sp. r4]]
	[[Category: Lee, C W]]		[[Category: Lee, C W]]

OCA at 08:34, 26 December 2018

OCA — Wed, 26 Dec 2018 08:34:29 GMT

←Older revision		Revision as of 08:34, 26 December 2018
Line 3:		Line 3:
	<StructureSection load='6agq' size='340' side='right' caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6agq' size='340' side='right' caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AGQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_sp._r4 Paenibacillus sp. r4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AGQ 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='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=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [http://pdbe.org/6agq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [http://www.ebi.ac.uk/pdbsum/6agq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq 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=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [http://pdbe.org/6agq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [http://www.ebi.ac.uk/pdbsum/6agq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cold-active acetyl xylan esterases allow for reduced bioreactor heating costs in bioenergy production. Here, we isolated and characterized a cold-active acetyl xylan esterase (PbAcE) from the psychrophilic soil microbe Paenibacillus sp. R4. The enzyme hydrolyzes glucose penta-acetate and xylan acetate, reversibly producing acetyl xylan from xylan, and it shows higher activity at 4 degrees C than at 25 degrees C. We solved the crystal structure of PbAcE at 2.1-A resolution to investigate its active site and the reason for its low-temperature activity. Structural analysis showed that PbAcE forms a hexamer with a central substrate binding tunnel, and the inter-subunit interactions are relatively weak compared with those of its mesophilic and thermophilic homologs. PbAcE also has a shorter loop and different residue composition in the beta4-alpha3 and beta5-alpha4 regions near the substrate binding site. Flexible subunit movements and different active site loop conformations may enable the strong low-temperature activity and broad substrate specificity of PbAcE. In addition, PbAcE was found to have strong activity against antibiotic compound substrates, such as cefotaxime and 7-amino cephalosporanic acid (7-ACA). In conclusion, the PbAcE structure and our biochemical results provide the first example of a cold-active acetyl xylan esterase and a starting template for structure-based protein engineering.
		+
		+	Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp.,Park SH, Yoo W, Lee CW, Jeong CS, Shin SC, Kim HW, Park H, Kim KK, Kim TD, Lee JH PLoS One. 2018 Oct 31;13(10):e0206260. doi: 10.1371/journal.pone.0206260., eCollection 2018. PMID:30379876<ref>PMID:30379876</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6agq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Paenibacillus sp. r4]]
	[[Category: Lee, C W]]		[[Category: Lee, C W]]
	[[Category: Lee, J H]]		[[Category: Lee, J H]]

OCA at 08:02, 10 October 2018

OCA — Wed, 10 Oct 2018 08:02:58 GMT

←Older revision		Revision as of 08:02, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6agq is ~~ON HOLD~~	+	==Acetyl xylan esterase from Paenibacillus sp. R4==
-		+	<StructureSection load='6agq' size='340' side='right' caption='[[6agq]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Park~~, S., ~~Lee~~, C.W., ~~Lee~~, J.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6agq]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AGQ FirstGlance]. <br>
-	~~Description: Acetyl xylan esterase from Paenibacillus sp. R4~~	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agq OCA], [http://pdbe.org/6agq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agq RCSB], [http://www.ebi.ac.uk/pdbsum/6agq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agq ProSAT]</span></td></tr>
-	[[Category: Lee, J.H]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lee, C W]]
		+	[[Category: Lee, J H]]
	[[Category: Park, S]]		[[Category: Park, S]]
-	[[Category: ~~Lee, C.W~~]]	+	[[Category: Acetyl esterase]]
		+	[[Category: Acetyl xylan esterase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Paenibacillus sp]]

OCA: Protected "6agq" [edit=sysop:move=sysop]

OCA — Wed, 22 Aug 2018 04:34:55 GMT

Protected "6agq" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:34, 22 August 2018

OCA: New page: '''Unreleased structure''' The entry 6agq is ON HOLD Authors: Park, S., Lee, C.W., Lee, J.H. Description: Acetyl xylan esterase from Paenibacillus sp. R4 [[Category: Unreleased Structu...

OCA — Wed, 22 Aug 2018 04:34:54 GMT

New page: '''Unreleased structure''' The entry 6agq is ON HOLD Authors: Park, S., Lee, C.W., Lee, J.H. Description: Acetyl xylan esterase from Paenibacillus sp. R4 [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 6agq is ON HOLD

Authors: Park, S., Lee, C.W., Lee, J.H.

Description: Acetyl xylan esterase from Paenibacillus sp. R4
[[Category: Unreleased Structures]]
[[Category: Lee, J.H]]
[[Category: Park, S]]
[[Category: Lee, C.W]]