6k1f - Revision history

OCA at 10:25, 22 November 2023

OCA — Wed, 22 Nov 2023 10:25:30 GMT

←Older revision		Revision as of 10:25, 22 November 2023
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	<StructureSection load='6k1f' size='340' side='right'caption='[[6k1f]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6k1f' size='340' side='right'caption='[[6k1f]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k1f]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33531 Atcc 33531~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K1F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6K1F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k1f]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Raoultella_planticola Raoultella planticola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K1F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>fucI, NCTC13095_01108 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~575 ATCC 33531])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/L-fucose_isomerase L-fucose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.25 5.3.1.25]~~ </~~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=6k1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1f OCA], [https://pdbe.org/6k1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k1f RCSB], [https://www.ebi.ac.uk/pdbsum/6k1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1f 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=6k1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1f OCA], [~~http~~://pdbe.org/6k1f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k1f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k1f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1f ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A443VNT1_RAOPL A0A443VNT1_RAOPL] Converts the aldose L-fucose into the corresponding ketose L-fuculose.[HAMAP-Rule:MF_01254]
	<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: Atcc 33531]]
-	[[Category: L-fucose isomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kim, D H~~]]	+	[[Category: Raoultella planticola]]
-	[[Category: Kim~~, I J~~]]	+	[[Category: Kim DH]]
-	[[Category: Kim~~, K H~~]]	+	[[Category: Kim IJ]]
-	[[Category: ~~Nam, K H~~]]	+	[[Category: Kim KH]]
-	[[Category: ~~Fucose]]~~	+	[[Category: Nam KH]]
-	~~[[Category: Isomerase~~]]	+

OCA at 11:21, 29 July 2020

OCA — Wed, 29 Jul 2020 11:21:43 GMT

←Older revision		Revision as of 11:21, 29 July 2020
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	==Crystal structure of the L-fucose isomerase from Raoultella sp.==		==Crystal structure of the L-fucose isomerase from Raoultella sp.==
-	<StructureSection load='6k1f' size='340' side='right'caption='[[6k1f]]' scene=''>	+	<StructureSection load='6k1f' size='340' side='right'caption='[[6k1f]], [[Resolution\|resolution]] 2.50Å' 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=6K1F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K1F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k1f]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33531 Atcc 33531]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K1F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K1F FirstGlance]. <br>
-	</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=6k1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1f OCA], [http://pdbe.org/6k1f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k1f RCSB], [http://www.ebi.ac.uk/pdbsum/6k1f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1f 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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fucI, NCTC13095_01108 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=575 ATCC 33531])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-fucose_isomerase L-fucose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.25 5.3.1.25] </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=6k1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1f OCA], [http://pdbe.org/6k1f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k1f RCSB], [http://www.ebi.ac.uk/pdbsum/6k1f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1f ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Background: l-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using l-fucose isomerase, which interconverts l-fucose and l-fuculose, can be an efficient way of producing l-fucose for industrial applications. Here, we performed biochemical and structural analyses of l-fucose isomerase identified from a novel species of Raoultella (RdFucI). Results: RdFucI exhibited higher enzymatic activity for l-fuculose than for l-fucose, and the rate for the reverse reaction of converting l-fuculose to l-fucose was higher than that for the forward reaction of converting l-fucose to l-fuculose. In the equilibrium mixture, a much higher proportion of l-fucose (~ ninefold) was achieved at 30 degrees C and pH 7, indicating that the enzyme-catalyzed reaction favors the formation of l-fucose from l-fuculose. When biochemical analysis was conducted using l-fuculose as the substrate, the optimal conditions for RdFucI activity were determined to be 40 degrees C and pH 10. However, the equilibrium composition was not affected by reaction temperature in the range of 30 to 50 degrees C. Furthermore, RdFucI was found to be a metalloenzyme requiring Mn(2+) as a cofactor. The comparative crystal structural analysis of RdFucI revealed the distinct conformation of alpha7-alpha8 loop of RdFucI. The loop is present at the entry of the substrate binding pocket and may affect the catalytic activity. Conclusions: RdFucI-catalyzed isomerization favored the reaction from l-fuculose to l-fucose. The biochemical and structural data of RdFucI will be helpful for the better understanding of the molecular mechanism of l-FucIs and the industrial production of l-fucose.
		+
		+	Enzymatic synthesis of l-fucose from l-fuculose using a fucose isomerase from Raoultella sp. and the biochemical and structural analyses of the enzyme.,Kim IJ, Kim DH, Nam KH, Kim KH Biotechnol Biofuels. 2019 Dec 5;12:282. doi: 10.1186/s13068-019-1619-0., eCollection 2019. PMID:31827610<ref>PMID:31827610</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k1f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33531]]
		+	[[Category: L-fucose isomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim DH]]	+	[[Category: Kim, D H]]
-	[[Category: Kim IJ]]	+	[[Category: Kim, I J]]
-	[[Category: Kim KH]]	+	[[Category: Kim, K H]]
-	[[Category: Nam KH]]	+	[[Category: Nam, K H]]
		+	[[Category: Fucose]]
		+	[[Category: Isomerase]]

OCA at 05:23, 13 May 2020

OCA — Wed, 13 May 2020 05:23:50 GMT

←Older revision		Revision as of 05:23, 13 May 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6k1f ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the L-fucose isomerase from Raoultella sp.==
-		+	<StructureSection load='6k1f' size='340' side='right'caption='[[6k1f]]' scene=''>
-	~~Authors~~: ~~Kim, I~~.J., ~~Kim, D~~.H., ~~Nam~~, K.H., ~~Kim, K~~.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K1F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K1F FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the L~~-~~fucose isomerase from Raoultella sp~~.	+	</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=6k1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1f OCA], [http://pdbe.org/6k1f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k1f RCSB], [http://www.ebi.ac.uk/pdbsum/6k1f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1f ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kim~~, D.H~~]]	+	__TOC__
-	[[Category: Kim~~, K.H~~]]	+	</StructureSection>
-	[[Category: Kim~~, I.J~~]]	+	[[Category: Large Structures]]
-	[[Category: Nam~~, K.H~~]]	+	[[Category: Kim DH]]
		+	[[Category: Kim IJ]]
		+	[[Category: Kim KH]]
		+	[[Category: Nam KH]]

OCA at 20:57, 5 June 2019

OCA — Wed, 05 Jun 2019 20:57:08 GMT

←Older revision		Revision as of 20:57, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k1f is ON HOLD	+	The entry 6k1f is ON HOLD until Paper Publication

	Authors: Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H.		Authors: Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H.
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	Description: Crystal structure of the L-fucose isomerase from Raoultella sp.		Description: Crystal structure of the L-fucose isomerase from Raoultella sp.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Kim, D.H]]
	[[Category: Kim, K.H]]		[[Category: Kim, K.H]]
	[[Category: Kim, I.J]]		[[Category: Kim, I.J]]
	[[Category: Nam, K.H]]		[[Category: Nam, K.H]]
-	[[Category: Kim, D.H]]

OCA: Protected "6k1f" [edit=sysop:move=sysop]

OCA — Tue, 21 May 2019 05:41:58 GMT

Protected "6k1f" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k1f is ON HOLD Authors: Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H. Description: Crystal structure of the L-fucose isomerase from Raoultella sp. [[...

OCA — Tue, 21 May 2019 05:41:56 GMT

New page: '''Unreleased structure''' The entry 6k1f is ON HOLD Authors: Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H. Description: Crystal structure of the L-fucose isomerase from Raoultella sp. [[...

New page

'''Unreleased structure'''

The entry 6k1f is ON HOLD

Authors: Kim, I.J., Kim, D.H., Nam, K.H., Kim, K.H.

Description: Crystal structure of the L-fucose isomerase from Raoultella sp.
[[Category: Unreleased Structures]]
[[Category: Kim, K.H]]
[[Category: Kim, I.J]]
[[Category: Nam, K.H]]
[[Category: Kim, D.H]]