5fu4 - Revision history

OCA at 13:26, 26 July 2023

OCA — Wed, 26 Jul 2023 13:26:43 GMT

←Older revision		Revision as of 13:26, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='5fu4' size='340' side='right'caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5fu4' size='340' side='right'caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_19208 Atcc 19208~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruminococcus_flavefaciens Ruminococcus flavefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BMA:BETA~~-~~D-MANNOSE'>BMA</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [~~http~~://pdbe.org/5fu4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fu4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fu4 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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [https://pdbe.org/5fu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [https://www.ebi.ac.uk/pdbsum/5fu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fu4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1A9TA80_RUMFL A0A1A9TA80_RUMFL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 19208]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Basle, A~~]]	+	[[Category: Ruminococcus flavefaciens]]
-	[[Category: ~~Gilbert, H J]]~~	+	[[Category: Basle A]]
-	~~[[Category: Luis,~~ A S]]	+	[[Category: Gilbert HJ]]
-	[[Category: ~~Venditto, I~~]]	+	[[Category: Luis AS]]
-	[[Category: ~~Carbohydrate binding module~~]]	+	[[Category: Venditto I]]
-	[[Category: ~~Cellulosome]]~~	+
-	~~[[Category: Endoglucanase cel5a]]~~	+
-	~~[[Category: Ruminoccocus flavefacien]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 07:37, 6 May 2020

OCA — Wed, 06 May 2020 07:37:12 GMT

←Older revision		Revision as of 07:37, 6 May 2020
Line 1:		Line 1:

	==The complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition==		==The complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition==
-	<StructureSection load='5fu4' size='340' side='right' caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5fu4' size='340' side='right'caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19208 Atcc 19208]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19208 Atcc 19208]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [http://pdbe.org/5fu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5fu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fu4 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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [http://pdbe.org/5fu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5fu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fu4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 19208]]		[[Category: Atcc 19208]]
		+	[[Category: Large Structures]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Gilbert, H J]]		[[Category: Gilbert, H J]]

OCA at 06:56, 28 March 2018

OCA — Wed, 28 Mar 2018 06:56:12 GMT

←Older revision		Revision as of 06:56, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5fu4' size='340' side='right' caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5fu4' size='340' side='right' caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19208 Atcc 19208]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</td></tr>
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Molecular mechanisms underlying~~ the ~~repair~~ of ~~nitrosylated [Fe-S] clusters~~ by the ~~microbial~~ protein ~~YtfE remain poorly understood~~. The X-~~ray~~ crystal ~~structure~~ of ~~YtfE~~, in ~~combination~~ with ~~EPR, magnetic circular dichroism (MCD), UV, and 17 O~~-~~labeling electron spin echo envelope modulation measurements~~, ~~show that each iron~~ of the ~~oxo~~-~~bridged FeII -FeIII diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates~~ and ~~two terminal histidines in addition to an oxo~~-~~bridge. Structural analysis reveals that there are two solvent-accessible tunnels~~, ~~both~~ of ~~which converge to~~ the ~~diiron center~~ and ~~are critical for capturing substrates~~. ~~The reactivity~~ of ~~the reduced~~-~~form FeII -FeII YtfE toward nitric oxide demonstrates~~ that the ~~prerequisite for N2 O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation~~ of ~~the two iron sites prior to their reductive coupling to produce N2 O is cooperative~~. This ~~result suggests~~ that, in ~~addition to any repair~~ of ~~iron centers (RIC) activity, YtfE acts as~~ an ~~NO-trapping scavenger to promote~~ the ~~NO to N2 O transformation under low NO flux, which precedes nitrosative stress~~.	+	The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens The data identified six previously unidentified CBM families that targeted beta-glucans, beta-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize beta-glucans and beta-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose.

-	~~Crystal Structure Analysis~~ of the ~~Repair of Iron Centers Protein YtfE and Its Interaction with NO~~.,~~Lo FC~~, ~~Hsieh CC~~, ~~Maestre-Reyna~~ M, ~~Chen CY~~, ~~Ko TP~~, ~~Horng YC~~, ~~Lai YC~~, ~~Chiang YW~~, ~~Chou CM~~, ~~Chiang CH~~, ~~Huang WN~~, ~~Lin YH~~, ~~Bohle DS~~, ~~Liaw WF Chemistry~~. 2016 Jun 1. ~~doi~~: ~~10.1002/chem.201600990~~. PMID:~~27246459~~<ref>PMID:~~27246459~~</ref>	+	Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition.,Venditto I, Luis AS, Rydahl M, Schuckel J, Fernandes VO, Vidal-Melgosa S, Bule P, Goyal A, Pires VM, Dourado CG, Ferreira LM, Coutinho PM, Henrissat B, Knox JP, Basle A, Najmudin S, Gilbert HJ, Willats WG, Fontes CM Proc Natl Acad Sci U S A. 2016 Jun 13. pii: 201601558. PMID:27298375<ref>PMID:27298375</ref>

	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>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 19208]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Gilbert, H J]]		[[Category: Gilbert, H J]]

OCA at 11:56, 14 July 2016

OCA — Thu, 14 Jul 2016 11:56:49 GMT

←Older revision		Revision as of 11:56, 14 July 2016
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the ~~portfolio~~ of ~~CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms~~ by ~~which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex,~~ the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein ~~modules of unknown function was used to determine the complete CBMome of R~~. ~~flavefaciens~~ The ~~data identified six previously unidentified CBM families that targeted beta~~-~~glucans, beta-mannans, and the pectic polysaccharide homogalacturonan. The~~ crystal ~~structures~~ of ~~four CBMs~~, in ~~conjunction~~ with ~~site~~-~~directed mutagenesis~~, ~~provide insight into the mechanism~~ of ~~ligand recognition. In~~ the ~~CBMs that recognize beta~~-~~glucans~~ and ~~beta~~-~~mannans~~, ~~differences in the conformation~~ of ~~conserved aromatic residues had a significant impact on~~ the ~~topology of the ligand binding cleft~~ and ~~thus ligand specificity~~. ~~A cluster~~ of ~~basic residues in CBM77 confers calcium~~-~~independent recognition of homogalacturonan, indicating~~ that the ~~carboxylates~~ of ~~galacturonic acid are key specificity determinants~~. This ~~report shows~~ that ~~the extended repertoire of proteins~~ in ~~the cellulosome~~ of ~~R. flavefaciens contributes to~~ an ~~extended CBMome that supports efficient PCW degradation in~~ the ~~absence of CBMs that specifically target crystalline cellulose~~.	+	Molecular mechanisms underlying the repair of nitrosylated [Fe-S] clusters by the microbial protein YtfE remain poorly understood. The X-ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and 17 O-labeling electron spin echo envelope modulation measurements, show that each iron of the oxo-bridged FeII -FeIII diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo-bridge. Structural analysis reveals that there are two solvent-accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced-form FeII -FeII YtfE toward nitric oxide demonstrates that the prerequisite for N2 O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N2 O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO-trapping scavenger to promote the NO to N2 O transformation under low NO flux, which precedes nitrosative stress.

-	~~Complexity~~ of the ~~Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition~~.,~~Venditto I~~, ~~Luis AS~~, ~~Rydahl~~ M, ~~Schuckel J~~, ~~Fernandes VO~~, ~~Vidal-Melgosa S~~, ~~Bule P~~, ~~Goyal A~~, ~~Pires VM~~, ~~Dourado CG~~, ~~Ferreira LM~~, ~~Coutinho PM~~, ~~Henrissat B~~, ~~Knox JP, Basle A, Najmudin S, Gilbert HJ, Willats WG, Fontes CM Proc Natl Acad Sci U S A~~. 2016 Jun 13. ~~pii~~: ~~201601558~~. PMID:~~27298375~~<ref>PMID:~~27298375~~</ref>	+	Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO.,Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF Chemistry. 2016 Jun 1. doi: 10.1002/chem.201600990. PMID:27246459<ref>PMID:27246459</ref>

	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>

OCA at 02:26, 13 July 2016

OCA — Wed, 13 Jul 2016 02:26:16 GMT

←Older revision		Revision as of 02:26, 13 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [http://pdbe.org/5fu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5fu4 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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [http://pdbe.org/5fu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5fu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fu4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:09, 23 June 2016

OCA — Thu, 23 Jun 2016 23:09:53 GMT

←Older revision		Revision as of 23:09, 23 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5fu4 is ~~ON HOLD until Paper~~ Publication	+	==The complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition==
		+	<StructureSection load='5fu4' size='340' side='right' caption='[[5fu4]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fu4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FU4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fu2\|5fu2]], [[5fu3\|5fu3]], [[5fu5\|5fu5]]</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=5fu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fu4 OCA], [http://pdbe.org/5fu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5fu4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens The data identified six previously unidentified CBM families that targeted beta-glucans, beta-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize beta-glucans and beta-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose.

-	~~Authors: Basle, A~~., Luis, A.S., ~~Venditto~~, I., Gilbert, H.J.	+	Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition.,Venditto I, Luis AS, Rydahl M, Schuckel J, Fernandes VO, Vidal-Melgosa S, Bule P, Goyal A, Pires VM, Dourado CG, Ferreira LM, Coutinho PM, Henrissat B, Knox JP, Basle A, Najmudin S, Gilbert HJ, Willats WG, Fontes CM Proc Natl Acad Sci U S A. 2016 Jun 13. pii: 201601558. PMID:27298375<ref>PMID:27298375</ref>

-	~~Description: The complexity~~ of the ~~Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Gilbert, H.J]]~~	+	<div class="pdbe-citations 5fu4" style="background-color:#fffaf0;"></div>
-	~~[[Category: Luis, A.S]]~~	+	== References ==
-	~~[[Category: Venditto, I]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Basle, A]]		[[Category: Basle, A]]
		+	[[Category: Gilbert, H J]]
		+	[[Category: Luis, A S]]
		+	[[Category: Venditto, I]]
		+	[[Category: Carbohydrate binding module]]
		+	[[Category: Cellulosome]]
		+	[[Category: Endoglucanase cel5a]]
		+	[[Category: Ruminoccocus flavefacien]]
		+	[[Category: Sugar binding protein]]

OCA at 00:46, 10 March 2016

OCA — Thu, 10 Mar 2016 00:46:53 GMT

←Older revision		Revision as of 00:46, 10 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fu4 is ON HOLD	+	The entry 5fu4 is ON HOLD until Paper Publication

	Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J.		Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J.

OCA at 15:33, 26 February 2016

OCA — Fri, 26 Feb 2016 15:33:24 GMT

←Older revision		Revision as of 15:33, 26 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fu4 is ON HOLD ~~until sometime in the future~~	+	The entry 5fu4 is ON HOLD

	Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J.		Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J.

OCA: Protected "5fu4" [edit=sysop:move=sysop]

OCA — Wed, 03 Feb 2016 13:26:16 GMT

Protected "5fu4" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:26, 3 February 2016

OCA: New page: '''Unreleased structure''' The entry 5fu4 is ON HOLD until sometime in the future Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J. Description: The complexity of the Ruminoc...

OCA — Wed, 03 Feb 2016 13:26:14 GMT

New page: '''Unreleased structure''' The entry 5fu4 is ON HOLD until sometime in the future Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J. Description: The complexity of the Ruminoc...

New page

'''Unreleased structure'''

The entry 5fu4 is ON HOLD until sometime in the future

Authors: Basle, A., Luis, A.S., Venditto, I., Gilbert, H.J.

Description: The complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition
[[Category: Unreleased Structures]]
[[Category: Gilbert, H.J]]
[[Category: Luis, A.S]]
[[Category: Venditto, I]]
[[Category: Basle, A]]