4mop - Revision history

OCA at 07:11, 27 November 2024

2024-11-27T07:11:55Z

← Older revision		Revision as of 07:11, 27 November 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12P:DODECAETHYLENE+GLYCOL'>12P</scene>, <scene name='pdbligand=2H5:3-DEOXY-3-FLUORO-BETA-D-GALACTOPYRANOSE'>2H5</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12P:DODECAETHYLENE+GLYCOL'>12P</scene>, <scene name='pdbligand=2H5:3-DEOXY-3-FLUORO-BETA-D-GALACTOPYRANOSE'>2H5</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [https://pdbe.org/4mop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [https://www.ebi.ac.uk/pdbsum/4mop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mop 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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [https://pdbe.org/4mop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [https://www.ebi.ac.uk/pdbsum/4mop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mop ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:58, 28 December 2022

2022-12-28T09:58:27Z

← Older revision		Revision as of 09:58, 28 December 2022
Line 1:		Line 1:

	==Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose==		==Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose==
	<StructureSection load='4mop' size='340' side='right' caption='[[4mop]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4mop' size='340' side='right'caption='[[4mop]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mop]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Coriolus_zonatus Coriolus zonatus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MOP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12P:DODECAETHYLENE+GLYCOL'>12P</scene>, <scene name='pdbligand=2H5:3-DEOXY-3-FLUORO-BETA-D-GALACTOPYRANOSE'>2H5</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene~~></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12P:DODECAETHYLENE+GLYCOL'>12P</scene>, <scene name='pdbligand=2H5:3-DEOXY-3-FLUORO-BETA-D-GALACTOPYRANOSE'>2H5</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igo\|2igo]], [[3pl8\|3pl8]], [[4moe\|4moe]], [[4mof\|4mof]], [[4mog\|4mog]], [[4moh\|4moh]], [[4moi\|4moi]], [[4moj\|4moj]], [[4mok\|4mok]], [[4mol\|4mol]], [[4mom\|4mom]], [[4moo\|4moo]], [[4moq\|4moq]], [[4mor\|4mor]], [[4mos\|4mos]]</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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [https://pdbe.org/4mop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [https://www.ebi.ac.uk/pdbsum/4mop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mop ProSAT]</span></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [~~http~~://pdbe.org/4mop PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mop PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mop ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q7ZA32_TRAOC Q7ZA32_TRAOC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Coriolus zonatus~~]]		[[Category: Large Structures]]
	[[Category: ~~Pyranose oxidase~~]]		[[Category: Trametes ochracea]]
	[[Category: Divne, C]]		[[Category: Divne C]]
	[[Category: Gandini, R]]		[[Category: Gandini R]]
	[[Category: Haltrich, D]]		[[Category: Haltrich D]]
	[[Category: Spadiut, O]]		[[Category: Spadiut O]]
	[[Category: Tan~~, T C]]~~		[[Category: Tan TC]]
	~~[[Category: Fad-binding]]~~
	~~[[Category: Flavinylation]]~~
	~~[[Category: Gmc oxidoreductase]]~~
	~~[[Category: Homotetramer]]~~
	~~[[Category: Intracellular]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Phbh fold]]~~
	~~[[Category: Substrate complex~~]]

OCA at 11:28, 4 August 2016

2016-08-04T11:28:37Z

← Older revision		Revision as of 11:28, 4 August 2016
Line 1:		Line 1:

	==Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose==		==Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose==
	<StructureSection load='4mop' size='340' side='right' caption='[[4mop]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4mop' size='340' side='right' caption='[[4mop]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [http://www.ebi.ac.uk/pdbsum/4mop 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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [http://pdbe.org/4mop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [http://www.ebi.ac.uk/pdbsum/4mop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mop ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4mop" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Pyranose oxidase\|Pyranose oxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:22, 21 December 2014

2014-12-21T18:22:50Z

← Older revision		Revision as of 18:22, 21 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_4mop~~\| ~~PDB~~=4mop \| ~~SCENE~~= }}		==Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose==
	===Pyranose 2-oxidase V546C ~~mutant~~ with 3-fluorinated galactose~~===~~		<StructureSection load='4mop' size='340' side='right' caption='[[4mop]], [[Resolution\|resolution]] 2.30Å' scene=''>
	~~{{ABSTRACT_PUBMED_24466218}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4mop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Coriolus_zonatus Coriolus zonatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MOP FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12P:DODECAETHYLENE+GLYCOL'>12P</scene>, <scene name='pdbligand=2H5:3-DEOXY-3-FLUORO-BETA-D-GALACTOPYRANOSE'>2H5</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igo\|2igo]], [[3pl8\|3pl8]], [[4moe\|4moe]], [[4mof\|4mof]], [[4mog\|4mog]], [[4moh\|4moh]], [[4moi\|4moi]], [[4moj\|4moj]], [[4mok\|4mok]], [[4mol\|4mol]], [[4mom\|4mom]], [[4moo\|4moo]], [[4moq\|4moq]], [[4mor\|4mor]], [[4mos\|4mos]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </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=4mop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mop RCSB], [http://www.ebi.ac.uk/pdbsum/4mop PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Each year, about six million tons of lactose are generated from liquid whey as industrial byproduct, and optimally this large carbohydrate waste should be used for the production of value-added products. Trametes multicolor pyranose 2-oxidase (TmP2O) catalyzes the oxidation of various monosaccharides to the corresponding 2-keto sugars. Thus, a potential use of TmP2O is to convert the products from lactose hydrolysis, D-glucose and D-galactose, to more valuable products such as tagatose. Oxidation of glucose is however strongly favored over galactose, and oxidation of both substrates at more equal rates is desirable. Characterization of TmP2O variants (H450G, V546C, H450G/V546C) with improved D-galactose conversion has been given earlier, of which H450G displayed the best relative conversion between the substrates. To rationalize the changes in conversion rates, we have analyzed high-resolution crystal structures of the aforementioned mutants with bound 2- and 3-fluorinated glucose and galactose. Binding of glucose and galactose in the productive 2-oxidation binding mode is nearly identical in all mutants, suggesting that this binding mode is essentially unaffected by the mutations. For the competing glucose binding mode, enzyme variants carrying the H450G replacement stabilize glucose as the alpha-anomer in position for 3-oxidation. The backbone relaxation at position 450 allows the substrate-binding loop to fold tightly around the ligand. V546C however stabilize glucose as the beta-anomer using an open loop conformation. Improved binding of galactose is enabled by subtle relaxation effects at key active-site backbone positions. The competing binding mode for galactose 2-oxidation by V546C stabilizes the beta-anomer for oxidation at C1, whereas H450G variants stabilize the 3-oxidation binding mode of the galactose alpha-anomer. The present study provides a detailed description of binding modes that rationalize changes in the relative conversion rates of D-glucose and D-galactose and can be used to refine future enzyme designs for more efficient use of lactose-hydrolysis byproducts.

	~~==About this Structure==~~		Structural Basis for Binding of Fluorinated Glucose and Galactose to Trametes multicolor Pyranose 2-Oxidase Variants with Improved Galactose Conversion.,Tan TC, Spadiut O, Gandini R, Haltrich D, Divne C PLoS One. 2014 Jan 21;9(1):e86736. doi: 10.1371/journal.pone.0086736. eCollection, 2014 Jan 21. PMID:24466218<ref>PMID:24466218</ref>
	~~[[4mop]] is a 4 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id=4MOP OCA].~~

	==~~Reference~~==		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~<ref group="xtra">PMID:024466218</ref>~~<references ~~group="xtra"~~/><~~references~~/>		</div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Coriolus zonatus]]
	[[Category: Pyranose oxidase]]		[[Category: Pyranose oxidase]]
	[[Category: Divne, C.]]		[[Category: Divne, C]]
	[[Category: Gandini, R.]]		[[Category: Gandini, R]]
	[[Category: Haltrich, D.]]		[[Category: Haltrich, D]]
	[[Category: Spadiut, O.]]		[[Category: Spadiut, O]]
	[[Category: Tan, T C.]]		[[Category: Tan, T C]]
	[[Category: Fad-binding]]		[[Category: Fad-binding]]
	[[Category: Flavinylation]]		[[Category: Flavinylation]]

OCA at 11:03, 5 February 2014

2014-02-05T11:03:19Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+{{STRUCTURE_4mop|  PDB=4mop  |  SCENE=  }}
-The entry 4mop is ON HOLD  until Paper Publication
+==About this Structure==
-Authors: Tan, T.C., Spadiut, O., Gandini, R., Haltrich, D., Divne, C.
+==Reference==
+<ref group="xtra">PMID:024466218</ref><references group="xtra"/><references/>
-Description: Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose
+[[Category: Pyranose oxidase]]

OCA at 06:57, 6 November 2013

2013-11-06T06:57:39Z

← Older revision		Revision as of 06:57, 6 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4mop is ON HOLD		The entry 4mop is ON HOLD until Paper Publication

	Authors: Tan, T.C., Spadiut, O., Gandini, R., Haltrich, D., Divne, C.		Authors: Tan, T.C., Spadiut, O., Gandini, R., Haltrich, D., Divne, C.

	Description: Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose		Description: Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose

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

2013-09-20T03:44:58Z

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

← Older revision	Revision as of 03:44, 20 September 2013
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4mop is ON HOLD Authors: Tan, T.C., Spadiut, O., Gandini, R., Haltrich, D., Divne, C. Description: Pyranose 2-oxidase V546C mutant with 3-fluorinat...

2013-09-20T03:44:57Z

New page: '''Unreleased structure''' The entry 4mop is ON HOLD Authors: Tan, T.C., Spadiut, O., Gandini, R., Haltrich, D., Divne, C. Description: Pyranose 2-oxidase V546C mutant with 3-fluorinat...

New page

'''Unreleased structure'''

The entry 4mop is ON HOLD

Authors: Tan, T.C., Spadiut, O., Gandini, R., Haltrich, D., Divne, C.

Description: Pyranose 2-oxidase V546C mutant with 3-fluorinated galactose