4kca - Revision history

OCA at 11:51, 30 November 2022

2022-11-30T11:51:48Z

←Older revision		Revision as of 11:51, 30 November 2022
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	<StructureSection load='4kca' size='340' side='right'caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4kca' size='340' side='right'caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kca]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KCA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kca]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kcb\|4kcb]]</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=4kca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kca OCA], [https://pdbe.org/4kca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kca RCSB], [https://www.ebi.ac.uk/pdbsum/4kca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kca 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=4kca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kca OCA], [~~http~~://pdbe.org/4kca PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kca RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kca PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kca ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arabinan endo-1,5-alpha-L-arabinosidase]]~~	+	[[Category: Bos taurus]]
-	~~[[Category: Bovin~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[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 09:49, 3 April 2019

2019-04-03T09:49:48Z

←Older revision		Revision as of 09:49, 3 April 2019
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	==Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library==		==Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library==
-	<StructureSection load='4kca' size='340' side='right' caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4kca' size='340' side='right'caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kca]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kca]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCA FirstGlance]. <br>
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Arabinanase\|Arabinanase]]	+	*[[Arabinanase 3D structures\|Arabinanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]		[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
	[[Category: Bovin]]		[[Category: Bovin]]
		+	[[Category: Large Structures]]
	[[Category: Costa, M C.M F]]		[[Category: Costa, M C.M F]]
	[[Category: Murakami, M T]]		[[Category: Murakami, M T]]

OCA at 19:31, 11 August 2016

2016-08-11T19:31:28Z

←Older revision		Revision as of 19:31, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library==		==Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library==
	<StructureSection load='4kca' size='340' side='right' caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4kca' size='340' side='right' caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kcb\|4kcb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kcb\|4kcb]]</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=4kca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kca RCSB], [http://www.ebi.ac.uk/pdbsum/4kca 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=4kca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kca OCA], [http://pdbe.org/4kca PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kca RCSB], [http://www.ebi.ac.uk/pdbsum/4kca PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kca ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4kca" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:34, 4 January 2015

2015-01-04T14:34:47Z

←Older revision		Revision as of 14:34, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4kca\| PDB=4kca \| SCENE= }}~~	+	==Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library==
-	===Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library===	+	<StructureSection load='4kca' size='340' side='right' caption='[[4kca]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24469445}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kca]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KCA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kc7\|4kc7]], [[4kc8\|4kc8]], [[4kcb\|4kcb]]</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=4kca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kca RCSB], [http://www.ebi.ac.uk/pdbsum/4kca 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>
-	~~[[4kca]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id=4KCA OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Arabinanase\|Arabinanase]]		*[[Arabinanase\|Arabinanase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024469445</ref>~~<references ~~group="xtra"~~/><~~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: Bovin]]
-	[[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 05:27, 9 April 2014

2014-04-09T05:27:04Z

←Older revision		Revision as of 05:27, 9 April 2014
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	==About this Structure==		==About this Structure==
	[[4kca]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA].		[[4kca]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA OCA].
		+
		+	==See Also==
		+	*[[Arabinanase\|Arabinanase]]

	==Reference==		==Reference==

OCA at 11:25, 5 February 2014

2014-02-05T11:25:40Z

←Older revision		Revision as of 11:25, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4kca\| PDB=4kca \| SCENE= }}
		+	===Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library===
		+	{{ABSTRACT_PUBMED_24469445}}

-	~~The entry~~ 4kca is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4kca]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCA 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 Endo~~-~~1,5-alpha-L-arabinanase from a 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 12:43, 20 November 2013

2013-11-20T12:43:14Z

←Older revision		Revision as of 12:43, 20 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4kca is ON HOLD	+	The entry 4kca 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 Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library		Description: Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

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

2013-05-02T07:16:03Z

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

←Older revision

Revision as of 07:16, 2 May 2013

OCA: New page: '''Unreleased structure''' The entry 4kca 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...

2013-05-02T07:16:02Z

New page: '''Unreleased structure''' The entry 4kca 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 4kca 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 Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library