7exu - Revision history

OCA at 10:54, 21 February 2024

OCA — Wed, 21 Feb 2024 10:54:30 GMT

←Older revision		Revision as of 10:54, 21 February 2024
Line 10:		Line 10:
	== 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;">
-	== 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 7exu" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:06, 29 November 2023

OCA — Wed, 29 Nov 2023 17:06:17 GMT

←Older revision		Revision as of 17:06, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7exu' size='340' side='right'caption='[[7exu]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='7exu' size='340' side='right'caption='[[7exu]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7exu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7exu]] 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=7EXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07Y:(2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol'>07Y</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]] 2.3Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07Y:(2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol'>07Y</scene>, <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=7exu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exu OCA], [https://pdbe.org/7exu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exu RCSB], [https://www.ebi.ac.uk/pdbsum/7exu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exu 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=7exu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exu OCA], [https://pdbe.org/7exu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exu RCSB], [https://www.ebi.ac.uk/pdbsum/7exu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exu 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 ==
Line 23:		Line 23:
	__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: Maruyama S]]
-	[[Category: Maruyama, S]]	+	[[Category: Yamada C]]
-	[[Category: Yamada, C]]	+
-	~~[[Category: Glycoside hydrolase family 127]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:11, 30 March 2022

OCA — Wed, 30 Mar 2022 11:11:56 GMT

←Older revision		Revision as of 11:11, 30 March 2022
Line 1:		Line 1:

	==GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside==		==GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside==
-	<StructureSection load='7exu' size='340' side='right'caption='[[7exu]]' scene=''>	+	<StructureSection load='7exu' size='340' side='right'caption='[[7exu]], [[Resolution\|resolution]] 2.30Å' 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=7EXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7exu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXU 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=7exu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exu OCA], [https://pdbe.org/7exu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exu RCSB], [https://www.ebi.ac.uk/pdbsum/7exu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exu 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=07Y:(2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol'>07Y</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=7exu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exu OCA], [https://pdbe.org/7exu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exu RCSB], [https://www.ebi.ac.uk/pdbsum/7exu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exu 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 7exu" 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: Maruyama S]]	+	[[Category: Fushinobu, S]]
-	[[Category: Yamada C]]	+	[[Category: Maruyama, S]]
		+	[[Category: Yamada, C]]
		+	[[Category: Glycoside hydrolase family 127]]
		+	[[Category: Hydrolase]]

OCA at 13:35, 17 November 2021

OCA — Wed, 17 Nov 2021 13:35:57 GMT

←Older revision		Revision as of 13:35, 17 November 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7exu is ~~ON HOLD until Paper Publication~~	+	==GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside==
-		+	<StructureSection load='7exu' size='340' side='right'caption='[[7exu]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EXU 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=7exu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7exu OCA], [https://pdbe.org/7exu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7exu RCSB], [https://www.ebi.ac.uk/pdbsum/7exu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7exu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Arakawa T]]
		+	[[Category: Fujita K]]
		+	[[Category: Fushinobu S]]
		+	[[Category: Maruyama S]]
		+	[[Category: Yamada C]]

OCA at 13:30, 17 June 2021

OCA — Thu, 17 Jun 2021 13:30:42 GMT

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

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

	Authors:		Authors:

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

OCA — Wed, 02 Jun 2021 13:26:40 GMT

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

←Older revision

Revision as of 13:26, 2 June 2021

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

OCA — Wed, 02 Jun 2021 13:26:39 GMT

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

New page

'''Unreleased structure'''

The entry 7exu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]