4kcb - Revision history

OCA at 11:51, 30 November 2022

2022-11-30T11:51:52Z

←Older revision		Revision as of 11:51, 30 November 2022
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	<StructureSection load='4kcb' size='340' side='right'caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4kcb' size='340' side='right'caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kcb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Uncultivated_bacterium Uncultivated~~ bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KCB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kcb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kca\|4kca]]</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=4kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcb OCA], [https://pdbe.org/4kcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcb RCSB], [https://www.ebi.ac.uk/pdbsum/4kcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcb ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </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=4kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcb OCA], [~~http~~://pdbe.org/4kcb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kcb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kcb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcb ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D2XML8_9BACT D2XML8_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Uncultivated~~ bacterium]]	+	[[Category: Uncultured bacterium]]
-	[[Category: Costa~~, M C.M F~~]]	+	[[Category: Costa MCMF]]
-	[[Category: Murakami~~, M T~~]]	+	[[Category: Murakami MT]]
-	[[Category: Nascimento~~, A F.Z~~]]	+	[[Category: Nascimento AFZ]]
-	[[Category: Polo~~, C C~~]]	+	[[Category: Polo CC]]
-	[[Category: Santos~~, C R~~]]	+	[[Category: Santos CR]]
-	[[Category: Wong~~, D W.S]]~~	+	[[Category: Wong DWS]]
-	~~[[Category: Arabinanase]]~~	+
-	~~[[Category: Beta-propeller]]~~	+
-	~~[[Category: Gh43]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:52, 3 April 2019

2019-04-03T08:52:08Z

←Older revision		Revision as of 08:52, 3 April 2019
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	==Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library==		==Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library==
-	<StructureSection load='4kcb' size='340' side='right' caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='4kcb' size='340' side='right'caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kcb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacterial_sp. Bacterial sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kcb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kca\|4kca]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kca\|4kca]]</td></tr>
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	</div>		</div>
	<div class="pdbe-citations 4kcb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4kcb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Arabinanase 3D structures\|Arabinanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]		[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
-	[[Category: ~~Bacterial sp~~]]	+	[[Category: Large Structures]]
		+	[[Category: Uncultivated bacterium]]
	[[Category: Costa, M C.M F]]		[[Category: Costa, M C.M F]]
	[[Category: Murakami, M T]]		[[Category: Murakami, M T]]

OCA at 20:42, 11 August 2016

2016-08-11T20:42:44Z

←Older revision		Revision as of 20:42, 11 August 2016
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		+
	==Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library==		==Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library==
	<StructureSection load='4kcb' size='340' side='right' caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4kcb' size='340' side='right' caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kca\|4kca]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kca\|4kca]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </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=4kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kcb RCSB], [http://www.ebi.ac.uk/pdbsum/4kcb 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=4kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcb OCA], [http://pdbe.org/4kcb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kcb RCSB], [http://www.ebi.ac.uk/pdbsum/4kcb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4kcb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:48, 4 January 2015

2015-01-04T13:48:15Z

←Older revision		Revision as of 13:48, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4kcb\| PDB=4kcb \| SCENE= }}~~	+	==Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library==
-	===Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library===	+	<StructureSection load='4kcb' size='340' side='right' caption='[[4kcb]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24469445}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kcb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacterial_sp. Bacterial sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kca\|4kca]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </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=4kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kcb RCSB], [http://www.ebi.ac.uk/pdbsum/4kcb PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmental friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation and catalysis of GH43 ABNs are presented. Biophysical, mutational and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically-relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg203-Ala230 loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation.

-	~~==About this Structure==~~	+	Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases.,Santos CR, Polo CC, Costa MC, Nascimento AF, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PS, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DW, Murakami MT J Biol Chem. 2014 Jan 27. PMID:24469445<ref>PMID:24469445</ref>
-	~~[[4kcb]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4KCB OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024469445</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]		[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
-	[[Category: Costa, M C.M F.]]	+	[[Category: Bacterial sp]]
-	[[Category: Murakami, M T.]]	+	[[Category: Costa, M C.M F]]
-	[[Category: Nascimento, A F.Z.]]	+	[[Category: Murakami, M T]]
-	[[Category: Polo, C C.]]	+	[[Category: Nascimento, A F.Z]]
-	[[Category: Santos, C R.]]	+	[[Category: Polo, C C]]
-	[[Category: Wong, D W.S.]]	+	[[Category: Santos, C R]]
		+	[[Category: Wong, D W.S]]
	[[Category: Arabinanase]]		[[Category: Arabinanase]]
	[[Category: Beta-propeller]]		[[Category: Beta-propeller]]

OCA at 11:16, 5 February 2014

2014-02-05T11:16:09Z

←Older revision		Revision as of 11:16, 5 February 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4kcb\| PDB=4kcb \| SCENE= }}
		+	===Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library===
		+	{{ABSTRACT_PUBMED_24469445}}

-	~~The entry~~ 4kcb is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4kcb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA].

-	~~Authors~~: ~~Santos, C.R., Polo, C.C.~~, Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S.~~, Murakami, M.T.~~	+	==Reference==
-		+	<ref group="xtra">PMID:024469445</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal Structure of Exo~~-~~1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library~~	+	[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
		+	[[Category: Costa, M C.M F.]]
		+	[[Category: Murakami, M T.]]
		+	[[Category: Nascimento, A F.Z.]]
		+	[[Category: Polo, C C.]]
		+	[[Category: Santos, C R.]]
		+	[[Category: Wong, D W.S.]]
		+	[[Category: Arabinanase]]
		+	[[Category: Beta-propeller]]
		+	[[Category: Gh43]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA at 13:10, 3 July 2013

2013-07-03T13:10:26Z

←Older revision		Revision as of 13:10, 3 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Santos, C.R., Polo, C.C., Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S., Murakami, M.T.		Authors: Santos, C.R., Polo, C.C., Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S., Murakami, M.T.

	Description: Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library		Description: Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

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

2013-05-02T07:16:04Z

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

←Older revision

Revision as of 07:16, 2 May 2013

OCA: New page: '''Unreleased structure''' The entry 4kcb is ON HOLD Authors: Santos, C.R., Polo, C.C., Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S., Murakami, M.T. Description: Crystal Structure...

2013-05-02T07:16:03Z

New page: '''Unreleased structure''' The entry 4kcb is ON HOLD Authors: Santos, C.R., Polo, C.C., Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S., Murakami, M.T. Description: Crystal Structure...

New page

'''Unreleased structure'''

The entry 4kcb is ON HOLD

Authors: Santos, C.R., Polo, C.C., Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S., Murakami, M.T.

Description: Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library