4ypj - Revision history

OCA at 09:04, 20 March 2024

OCA — Wed, 20 Mar 2024 09:04:03 GMT

←Older revision		Revision as of 09:04, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YPJ 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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [https://pdbe.org/4ypj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [https://www.ebi.ac.uk/pdbsum/4ypj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypj 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]] 2.5Å</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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [https://pdbe.org/4ypj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [https://www.ebi.ac.uk/pdbsum/4ypj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/E5RWQ2_NIACI E5RWQ2_NIACI]		[https://www.uniprot.org/uniprot/E5RWQ2_NIACI E5RWQ2_NIACI]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	beta-galactosidase (EC3.2.1.23) from Bacillus circulans ATCC 31382, designated BgaD, exhibits high transglycosylation activity to produce galacto-oligosaccharides. BgaD has been speculated to have a multiple domain architecture including a F5/8 type C domain or a discoidin (DS) domain in the C-terminal peptide region from amino acid sequence analysis. Here, we solved the first crystal structure of the C-terminal deletion mutant BgaD-D, consisting of sugar binding, Glyco_hydro, catalytic, and bacterial Ig-like domains, at 2.5 A. In the asymmetric unit, two molecules of BgaD-D were identified and the value of VM was estimated to be 5.0 A3 /Da. It had been speculated that the structure of BgaD-D consists of four domains. From the structural analysis, however, we clarified that BgaD-D consists of five domains. We identified a new domain structure comprised of beta-sheets in BgaD. The catalytic domain exhibits a TIM barrel structure with a small pocket suited for accommodating the disaccharides. Detailed structural information for the amino acid residues related to activity and substrate specificity was clarified in the catalytic domain. Furthermore, using the structural information, we successfully constructed some thermostable mutants via protein engineering method. This article is protected by copyright. All rights reserved.
-
-	Crystal structure of beta-galactosidase from Bacillus circulans ATCC 31382 (BgaD) and the construction of the thermophilic mutants.,Ishikawa K, Kataoka M, Yanamoto T, Nakabayashi M, Watanabe M, Ishihara S, Yamaguchi S FEBS J. 2015 Apr 16. doi: 10.1111/febs.13298. PMID:25879162<ref>PMID:25879162</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]		*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:24, 3 May 2023

OCA — Wed, 03 May 2023 08:24:42 GMT

←Older revision		Revision as of 08:24, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4ypj' size='340' side='right'caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ypj' size='340' side='right'caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [https://pdbe.org/4ypj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [https://www.ebi.ac.uk/pdbsum/4ypj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypj 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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [~~http~~://pdbe.org/4ypj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ypj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E5RWQ2_NIACI E5RWQ2_NIACI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishikawa, K]]	+	[[Category: Niallia circulans]]
-	[[Category: Kataoka, M]]	+	[[Category: Ishikawa K]]
-	[[Category: Nakabayashi, M]]	+	[[Category: Kataoka M]]
-	[[Category: Watanabe, M]]	+	[[Category: Nakabayashi M]]
-	[[Category: Yanamoto, T]]	+	[[Category: Watanabe M]]
-	~~[[Category: Glycoside hydrolase]]~~	+	[[Category: Yanamoto T]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:42, 4 March 2020

OCA — Wed, 04 Mar 2020 07:42:18 GMT

←Older revision		Revision as of 07:42, 4 March 2020
Line 1:		Line 1:

	==X-ray Structure of The Mutant of Glycoside Hydrolase==		==X-ray Structure of The Mutant of Glycoside Hydrolase==
-	<StructureSection load='4ypj' size='340' side='right' caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4ypj' size='340' side='right'caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
		+	[[Category: Large Structures]]
	[[Category: Ishikawa, K]]		[[Category: Ishikawa, K]]
	[[Category: Kataoka, M]]		[[Category: Kataoka, M]]

OCA at 12:05, 16 November 2017

OCA — Thu, 16 Nov 2017 12:05:16 GMT

←Older revision		Revision as of 12:05, 16 November 2017
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:45, 3 August 2017

OCA — Thu, 03 Aug 2017 10:45:22 GMT

←Older revision		Revision as of 10:45, 3 August 2017
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ypj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:28, 19 April 2017

OCA — Wed, 19 Apr 2017 13:28:39 GMT

←Older revision		Revision as of 13:28, 19 April 2017
Line 1:		Line 1:
		+
	==X-ray Structure of The Mutant of Glycoside Hydrolase==		==X-ray Structure of The Mutant of Glycoside Hydrolase==
	<StructureSection load='4ypj' size='340' side='right' caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ypj' size='340' side='right' caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [http://www.ebi.ac.uk/pdbsum/4ypj 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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [http://pdbe.org/4ypj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [http://www.ebi.ac.uk/pdbsum/4ypj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypj 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 4ypj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:38, 30 April 2015

OCA — Thu, 30 Apr 2015 11:38:17 GMT

←Older revision		Revision as of 11:38, 30 April 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==X-ray Structure of The Mutant of Glycoside Hydrolase==
		+	<StructureSection load='4ypj' size='340' side='right' caption='[[4ypj]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ypj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPJ FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=4ypj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ypj RCSB], [http://www.ebi.ac.uk/pdbsum/4ypj PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta-galactosidase (EC3.2.1.23) from Bacillus circulans ATCC 31382, designated BgaD, exhibits high transglycosylation activity to produce galacto-oligosaccharides. BgaD has been speculated to have a multiple domain architecture including a F5/8 type C domain or a discoidin (DS) domain in the C-terminal peptide region from amino acid sequence analysis. Here, we solved the first crystal structure of the C-terminal deletion mutant BgaD-D, consisting of sugar binding, Glyco_hydro, catalytic, and bacterial Ig-like domains, at 2.5 A. In the asymmetric unit, two molecules of BgaD-D were identified and the value of VM was estimated to be 5.0 A3 /Da. It had been speculated that the structure of BgaD-D consists of four domains. From the structural analysis, however, we clarified that BgaD-D consists of five domains. We identified a new domain structure comprised of beta-sheets in BgaD. The catalytic domain exhibits a TIM barrel structure with a small pocket suited for accommodating the disaccharides. Detailed structural information for the amino acid residues related to activity and substrate specificity was clarified in the catalytic domain. Furthermore, using the structural information, we successfully constructed some thermostable mutants via protein engineering method. This article is protected by copyright. All rights reserved.

-	~~The entry 4ypj is ON HOLD~~	+	Crystal structure of beta-galactosidase from Bacillus circulans ATCC 31382 (BgaD) and the construction of the thermophilic mutants.,Ishikawa K, Kataoka M, Yanamoto T, Nakabayashi M, Watanabe M, Ishihara S, Yamaguchi S FEBS J. 2015 Apr 16. doi: 10.1111/febs.13298. PMID:25879162<ref>PMID:25879162</ref>

-	~~Authors: Ishikawa~~, K.~~, Kataoka, M~~.~~, Yanamoto, T., Nakabayashi, M., Watanabe, M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: X-~~ray Structure of The Mutant of Glycoside Hydrolase~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-galactosidase]]
		+	[[Category: Ishikawa, K]]
		+	[[Category: Kataoka, M]]
		+	[[Category: Nakabayashi, M]]
	[[Category: Watanabe, M]]		[[Category: Watanabe, M]]
-	[[Category: Nakabayashi, M]]
	[[Category: Yanamoto, T]]		[[Category: Yanamoto, T]]
-	[[Category: ~~Ishikawa, K~~]]	+	[[Category: Glycoside hydrolase]]
-	[[Category: ~~Kataoka, M~~]]	+	[[Category: Hydrolase]]

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

OCA — Wed, 18 Mar 2015 11:00:43 GMT

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

←Older revision

Revision as of 11:00, 18 March 2015

OCA: New page: '''Unreleased structure''' The entry 4ypj is ON HOLD Authors: Ishikawa, K., Kataoka, M., Yanamoto, T., Nakabayashi, M., Watanabe, M. Description: X-ray Structure of The Mutant of Glyco...

OCA — Wed, 18 Mar 2015 11:00:42 GMT

New page: '''Unreleased structure''' The entry 4ypj is ON HOLD Authors: Ishikawa, K., Kataoka, M., Yanamoto, T., Nakabayashi, M., Watanabe, M. Description: X-ray Structure of The Mutant of Glyco...

New page

'''Unreleased structure'''

The entry 4ypj is ON HOLD

Authors: Ishikawa, K., Kataoka, M., Yanamoto, T., Nakabayashi, M., Watanabe, M.

Description: X-ray Structure of The Mutant of Glycoside Hydrolase
[[Category: Unreleased Structures]]
[[Category: Watanabe, M]]
[[Category: Nakabayashi, M]]
[[Category: Yanamoto, T]]
[[Category: Ishikawa, K]]
[[Category: Kataoka, M]]