4w7i - Revision history

OCA at 15:21, 8 November 2023

2023-11-08T15:21:43Z

←Older revision		Revision as of 15:21, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7I FirstGlance]. <br>		<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7I 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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [https://pdbe.org/4w7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [https://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</span></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]] 1.98Å</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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [https://pdbe.org/4w7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [https://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 06:56, 7 April 2023

2023-04-07T06:56:10Z

←Older revision		Revision as of 06:56, 7 April 2023
Line 3:		Line 3:
	<StructureSection load='4w7i' size='340' side='right'caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='4w7i' size='340' side='right'caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sphingomonas_sp.~~_a1~~ Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4W7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7I FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</td></tr>~~	+	</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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [https://pdbe.org/4w7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [https://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [~~http~~://pdbe.org/4w7i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A096LNF1_9SPHN A0A096LNF1_9SPHN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sphingomonas sp. a1]]	+	[[Category: Sphingomonas sp. A1]]
-	[[Category: Hashimoto, W]]	+	[[Category: Hashimoto W]]
-	[[Category: Kawai, S]]	+	[[Category: Kawai S]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Murata, K]]	+	[[Category: Murata K]]
-	[[Category: Takase, R]]	+	[[Category: Takase R]]
-	~~[[Category: Alginate metabolism]]~~	+
-	~~[[Category: Alpha/beta/alpha]]~~	+
-	~~[[Category: Loop-exchange]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann-fold]]~~	+
-	~~[[Category: Short-chain dehydrogenase/reductase~~]]	+

OCA at 08:01, 23 May 2019

2019-05-23T08:01:07Z

←Older revision		Revision as of 08:01, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of DEH reductase A1-R' mutant==		==Crystal structure of DEH reductase A1-R' mutant==
-	<StructureSection load='4w7i' size='340' side='right' caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='4w7i' size='340' side='right'caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://pdbe.org/4w7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://pdbe.org/4w7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sphingomonas sp. a1]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Kawai, S]]		[[Category: Kawai, S]]

OCA at 01:12, 19 January 2017

2017-01-19T01:12:24Z

←Older revision		Revision as of 01:12, 19 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of DEH reductase A1-R' mutant==		==Crystal structure of DEH reductase A1-R' mutant==
	<StructureSection load='4w7i' size='340' side='right' caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='4w7i' size='340' side='right' caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>		<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i 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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://pdbe.org/4w7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4w7i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:08, 10 December 2014

2014-12-10T12:08:50Z

←Older revision		Revision as of 12:08, 10 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>		<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i 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=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-d-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family. A1-R-deficient cells produced another DEH reductase, designated A1-R', with a preference for NADH. Here, we show the identification of a novel NADH-dependent DEH reductase A1-R' in strain A1, structural determination of A1-R' by x-ray crystallography, and structure-based conversion of a coenzyme requirement in SDR enzymes, A1-R and A1-R'. A1-R' was purified from strain A1 cells and enzymatically characterized. Except for the coenzyme requirement, there was no significant difference in enzyme characteristics between A1-R and A1-R'. Crystal structures of A1-R' and A1-R'.NAD(+) complex were determined at 1.8 and 2.7 A resolutions, respectively. Because of a 64% sequence identity, overall structures of A1-R' and A1-R were similar, although a difference in the coenzyme-binding site (particularly the nucleoside ribose 2' region) was observed. Distinct from A1-R, A1-R' included a negatively charged, shallower binding site. These differences were caused by amino acid residues on the two loops around the site. The A1-R' mutant with the two A1-R-typed loops maintained potent enzyme activity with specificity for NADPH rather than NADH, demonstrating that the two loops determine the coenzyme requirement, and loop exchange is a promising method for conversion of coenzyme requirement in the SDR family.
		+
		+	Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism.,Takase R, Mikami B, Kawai S, Murata K, Hashimoto W J Biol Chem. 2014 Nov 28;289(48):33198-214. doi: 10.1074/jbc.M114.585661. Epub, 2014 Oct 6. PMID:25288804<ref>PMID:25288804</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Hashimoto, W.]]	+	[[Category: Hashimoto, W]]
-	[[Category: Kawai, S.]]	+	[[Category: Kawai, S]]
-	[[Category: Mikami, B.]]	+	[[Category: Mikami, B]]
-	[[Category: Murata, K.]]	+	[[Category: Murata, K]]
-	[[Category: Takase, R.]]	+	[[Category: Takase, R]]
	[[Category: Alginate metabolism]]		[[Category: Alginate metabolism]]
	[[Category: Alpha/beta/alpha]]		[[Category: Alpha/beta/alpha]]

OCA at 10:53, 24 September 2014

2014-09-24T10:53:55Z

←Older revision		Revision as of 10:53, 24 September 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of DEH reductase A1-R' mutant==
-		+	<StructureSection load='4w7i' size='340' side='right' caption='[[4w7i]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~The entry~~ 4w7i is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4w7i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7I FirstGlance]. <br>
-	~~Authors~~: ~~Takase~~, R., ~~Mikami~~, B., Kawai, S., Murata, K., ~~Hashimoto, W~~.	+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tkl\|4tkl]], [[4w7h\|4w7h]]</td></tr>
-		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w7i RCSB], [http://www.ebi.ac.uk/pdbsum/4w7i PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal structure of DEH reductase A1~~-~~R' mutant~~	+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hashimoto, W.]]
		+	[[Category: Kawai, S.]]
		+	[[Category: Mikami, B.]]
		+	[[Category: Murata, K.]]
		+	[[Category: Takase, R.]]
		+	[[Category: Alginate metabolism]]
		+	[[Category: Alpha/beta/alpha]]
		+	[[Category: Loop-exchange]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann-fold]]
		+	[[Category: Short-chain dehydrogenase/reductase]]

OCA: Protected "4w7i" [edit=sysop:move=sysop]

2014-08-27T07:32:29Z

Protected "4w7i" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:32, 27 August 2014

OCA: New page: '''Unreleased structure''' The entry 4w7i is ON HOLD Authors: Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W. Description: Crystal structure of DEH reductase A1-R' mutant

2014-08-27T07:32:28Z

New page: '''Unreleased structure''' The entry 4w7i is ON HOLD Authors: Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W. Description: Crystal structure of DEH reductase A1-R' mutant

New page

'''Unreleased structure'''

The entry 4w7i is ON HOLD

Authors: Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W.

Description: Crystal structure of DEH reductase A1-R' mutant