7exw - Revision history

OCA at 17:06, 29 November 2023

2023-11-29T17:06:20Z

←Older revision		Revision as of 17:06, 29 November 2023
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	<StructureSection load='7exw' size='340' side='right'caption='[[7exw]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='7exw' size='340' side='right'caption='[[7exw]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7exw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7exw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum_JCM_1217 Bifidobacterium longum subsp. longum JCM 1217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=09X:2-bromanyl-N-[(2R,3R,4R,5S}-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide'>09X</scene>, <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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7exu\|7exu]], [[7exv\|7exv]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=09X:2-bromanyl-N-[(2R,3R,4R,5S}-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide'>09X</scene>, <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'>[https://en.wikipedia.org/wiki/Non-reducing_end_beta-L-arabinofuranosidase Non-reducing end beta-L-arabinofuranosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.185 3.2.1.185] </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=7exw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exw OCA], [https://pdbe.org/7exw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exw RCSB], [https://www.ebi.ac.uk/pdbsum/7exw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exw 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=7exw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exw OCA], [https://pdbe.org/7exw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exw RCSB], [https://www.ebi.ac.uk/pdbsum/7exw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HYBA1_BIFL2 HYBA1_BIFL2]] Beta-L-arabinofuranosidase that removes the beta-L-arabinofuranose residue from the non-reducing end of various substrates, including beta-L-arabinofuranosyl-hydroxyproline (Ara-Hyp), Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), Ara-beta-1,2-Ara-beta-1,2-Ara-beta-Hyp (Ara(3)-Hyp), and beta-L-arabinofuranosyl-(1->2)-1-O-methyl-beta-L-arabinofuranose. In the presence of 1-alkanols, shows transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.	+	[https://www.uniprot.org/uniprot/HYBA1_BIFL2 HYBA1_BIFL2] Beta-L-arabinofuranosidase that removes the beta-L-arabinofuranose residue from the non-reducing end of various substrates, including beta-L-arabinofuranosyl-hydroxyproline (Ara-Hyp), Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), Ara-beta-1,2-Ara-beta-1,2-Ara-beta-Hyp (Ara(3)-Hyp), and beta-L-arabinofuranosyl-(1->2)-1-O-methyl-beta-L-arabinofuranose. In the presence of 1-alkanols, shows transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.
	<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: Bifidobacterium longum subsp. longum JCM 1217]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Non-reducing end beta-L-arabinofuranosidase]]~~	+	[[Category: Arakawa T]]
-	[[Category: Arakawa, T]]	+	[[Category: Fujita K]]
-	[[Category: Fujita, K]]	+	[[Category: Fushinobu S]]
-	[[Category: Fushinobu, S]]	+	[[Category: Sawano K]]
-	[[Category: Sawano, K]]	+	[[Category: Yamada C]]
-	[[Category: Yamada, C]]	+
-	~~[[Category: Glycoside hydrolase family 127]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:12, 30 March 2022

2022-03-30T11:12:04Z

←Older revision		Revision as of 11:12, 30 March 2022
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	==GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with alpha-L-arabinofuranosylamide==		==GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with alpha-L-arabinofuranosylamide==
-	<StructureSection load='7exw' size='340' side='right'caption='[[7exw]]' scene=''>	+	<StructureSection load='7exw' size='340' side='right'caption='[[7exw]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7exw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXW FirstGlance]. <br>
-	</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=7exw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exw OCA], [https://pdbe.org/7exw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exw RCSB], [https://www.ebi.ac.uk/pdbsum/7exw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exw ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=09X:2-bromanyl-N-[(2R,3R,4R,5S}-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide'>09X</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7exu\|7exu]], [[7exv\|7exv]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Non-reducing_end_beta-L-arabinofuranosidase Non-reducing end beta-L-arabinofuranosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.185 3.2.1.185] </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=7exw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exw OCA], [https://pdbe.org/7exw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exw RCSB], [https://www.ebi.ac.uk/pdbsum/7exw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/HYBA1_BIFL2 HYBA1_BIFL2]] Beta-L-arabinofuranosidase that removes the beta-L-arabinofuranose residue from the non-reducing end of various substrates, including beta-L-arabinofuranosyl-hydroxyproline (Ara-Hyp), Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), Ara-beta-1,2-Ara-beta-1,2-Ara-beta-Hyp (Ara(3)-Hyp), and beta-L-arabinofuranosyl-(1->2)-1-O-methyl-beta-L-arabinofuranose. In the presence of 1-alkanols, shows transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-beta-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, beta-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas alpha-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the beta-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
		+
		+	Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase.,Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S Glycobiology. 2021 Oct 7. pii: 6382528. doi: 10.1093/glycob/cwab103. PMID:34735571<ref>PMID:34735571</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7exw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arakawa T]]	+	[[Category: Non-reducing end beta-L-arabinofuranosidase]]
-	[[Category: Fujita K]]	+	[[Category: Arakawa, T]]
-	[[Category: Fushinobu S]]	+	[[Category: Fujita, K]]
-	[[Category: Sawano K]]	+	[[Category: Fushinobu, S]]
-	[[Category: Yamada C]]	+	[[Category: Sawano, K]]
		+	[[Category: Yamada, C]]
		+	[[Category: Glycoside hydrolase family 127]]
		+	[[Category: Hydrolase]]

OCA at 13:36, 17 November 2021

2021-11-17T13:36:02Z

←Older revision		Revision as of 13:36, 17 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7exw is ~~ON HOLD until Paper Publication~~	+	==GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with alpha-L-arabinofuranosylamide==
-		+	<StructureSection load='7exw' size='340' side='right'caption='[[7exw]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXW FirstGlance]. <br>
-	~~Description~~:	+	</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=7exw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exw OCA], [https://pdbe.org/7exw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exw RCSB], [https://www.ebi.ac.uk/pdbsum/7exw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Arakawa T]]
		+	[[Category: Fujita K]]
		+	[[Category: Fushinobu S]]
		+	[[Category: Sawano K]]
		+	[[Category: Yamada C]]

OCA at 13:30, 17 June 2021

2021-06-17T13:30:44Z

←Older revision		Revision as of 13:30, 17 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7exw is ON HOLD	+	The entry 7exw is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7exw" [edit=sysop:move=sysop]

2021-06-09T10:58:18Z

Protected "7exw" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:58, 9 June 2021

OCA: New page: '''Unreleased structure''' The entry 7exw is ON HOLD Authors: Description: Category: Unreleased Structures

2021-06-09T10:58:17Z

New page: '''Unreleased structure''' The entry 7exw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7exw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]