8bgn - Revision history

OCA at 08:18, 7 February 2024

OCA — Wed, 07 Feb 2024 08:18:14 GMT

←Older revision		Revision as of 08:18, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8bgn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_chitonophagus Thermococcus chitonophagus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[8bgn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_chitonophagus Thermococcus chitonophagus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BGN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.76Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=8bgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bgn OCA], [https://pdbe.org/8bgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bgn RCSB], [https://www.ebi.ac.uk/pdbsum/8bgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bgn 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=8bgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bgn OCA], [https://pdbe.org/8bgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bgn RCSB], [https://www.ebi.ac.uk/pdbsum/8bgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bgn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A160VQZ8_9EURY A0A160VQZ8_9EURY]		[https://www.uniprot.org/uniprot/A0A160VQZ8_9EURY A0A160VQZ8_9EURY]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Chitin is a major source of energy and macroelements for many organisms. An important step in its degradation is the deacetylation of chitin or its fragments. Deacetylase from the extremophile Pyrococcus chitonophagus has been analyzed by X-ray crystallography, small-angle X-ray scattering, differential scanning calorimetry, isothermal titration calorimetry and NMR to determine its structure, thermodynamics and enzymatic properties. It is a hexameric, zinc-containing metalloenzyme that retains its structural integrity up to temperatures slightly exceeding 100 degrees C. It removes the acetyl group specifically from the non-reducing end of the sugar substrate. Its main substrate is N,N-diacetylchitobiose but it also active, at a reduced level, toward N-acetyl-d-glucosamine or a trimer of N-acetyl-d-glucosamine units. Crystallographic analysis includes the structure of the enzyme with its main substrate approaching the active site in a monodentate manner, replacing the single water molecule that is bound at the Zn(2+) cation when the ligand is absent. The Zn(2+) cation remains tetrahedrally coordinated, with three of its ligands provided by the protein's conserved His-Asp-His triad. The crystal structures are consistent with the reaction mechanism proceeding via an anhydride intermediate. Hydrolysis as the first step cannot be ruled out in a hydrated environment but no defined 'hydrolytic water' site can be identified in the analyzed structures.
-
-	Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.,Biniek-Antosiak K, Bejger M, Sliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W Int J Mol Sci. 2022 Dec 12;23(24):15736. doi: 10.3390/ijms232415736. PMID:36555375<ref>PMID:36555375</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8bgn" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:39, 11 January 2023

OCA — Wed, 11 Jan 2023 07:39:59 GMT

←Older revision		Revision as of 07:39, 11 January 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8bgn is ~~ON HOLD until Paper~~ Publication	+	==N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus==
		+	<StructureSection load='8bgn' size='340' side='right'caption='[[8bgn]], [[Resolution\|resolution]] 2.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8bgn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_chitonophagus Thermococcus chitonophagus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BGN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=8bgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bgn OCA], [https://pdbe.org/8bgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bgn RCSB], [https://www.ebi.ac.uk/pdbsum/8bgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bgn ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A160VQZ8_9EURY A0A160VQZ8_9EURY]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chitin is a major source of energy and macroelements for many organisms. An important step in its degradation is the deacetylation of chitin or its fragments. Deacetylase from the extremophile Pyrococcus chitonophagus has been analyzed by X-ray crystallography, small-angle X-ray scattering, differential scanning calorimetry, isothermal titration calorimetry and NMR to determine its structure, thermodynamics and enzymatic properties. It is a hexameric, zinc-containing metalloenzyme that retains its structural integrity up to temperatures slightly exceeding 100 degrees C. It removes the acetyl group specifically from the non-reducing end of the sugar substrate. Its main substrate is N,N-diacetylchitobiose but it also active, at a reduced level, toward N-acetyl-d-glucosamine or a trimer of N-acetyl-d-glucosamine units. Crystallographic analysis includes the structure of the enzyme with its main substrate approaching the active site in a monodentate manner, replacing the single water molecule that is bound at the Zn(2+) cation when the ligand is absent. The Zn(2+) cation remains tetrahedrally coordinated, with three of its ligands provided by the protein's conserved His-Asp-His triad. The crystal structures are consistent with the reaction mechanism proceeding via an anhydride intermediate. Hydrolysis as the first step cannot be ruled out in a hydrated environment but no defined 'hydrolytic water' site can be identified in the analyzed structures.

-	~~Authors~~:	+	Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.,Biniek-Antosiak K, Bejger M, Sliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W Int J Mol Sci. 2022 Dec 12;23(24):15736. doi: 10.3390/ijms232415736. PMID:36555375<ref>PMID:36555375</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8bgn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Thermococcus chitonophagus]]
		+	[[Category: Bejger M]]
		+	[[Category: Biniek-Antosiak K]]
		+	[[Category: Rypniewski W]]

OCA at 08:19, 30 November 2022

OCA — Wed, 30 Nov 2022 08:19:13 GMT

←Older revision		Revision as of 08:19, 30 November 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8bgn is ON HOLD	+	The entry 8bgn is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8bgn" [edit=sysop:move=sysop]

OCA — Wed, 09 Nov 2022 04:51:28 GMT

Protected "8bgn" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:51, 9 November 2022

OCA: New page: '''Unreleased structure''' The entry 8bgn is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 Nov 2022 04:51:26 GMT

New page: '''Unreleased structure''' The entry 8bgn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8bgn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]