4xpp - Revision history

OCA at 15:30, 8 November 2023

2023-11-08T15:30:11Z

←Older revision		Revision as of 15:30, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudopedobacter_saltans Pseudopedobacter saltans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudopedobacter_saltans Pseudopedobacter saltans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [https://pdbe.org/4xpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [https://www.ebi.ac.uk/pdbsum/4xpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpp 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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [https://pdbe.org/4xpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [https://www.ebi.ac.uk/pdbsum/4xpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpp ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:46, 26 April 2023

2023-04-26T17:46:50Z

←Older revision		Revision as of 17:46, 26 April 2023
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	<StructureSection load='4xpp' size='340' side='right'caption='[[4xpp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xpp' size='340' side='right'caption='[[4xpp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ccug_39354 Ccug 39354~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudopedobacter_saltans Pseudopedobacter saltans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xpo\|4xpo]], [[4xpq\|4xpq]], [[4xpr\|4xpr]], [[4xps\|4xps]]</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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [https://pdbe.org/4xpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [https://www.ebi.ac.uk/pdbsum/4xpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpp ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [~~http~~://pdbe.org/4xpp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xpp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpp ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0F7R6D6_9SPHI A0A0F7R6D6_9SPHI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alpha-galactosidase]]
-	[[Category: Ccug 39354]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ichikawa, M]]	+	[[Category: Pseudopedobacter saltans]]
-	[[Category: Ishizaki, Y]]	+	[[Category: Ichikawa M]]
-	[[Category: Miyazaki, T]]	+	[[Category: Ishizaki Y]]
-	[[Category: Nishikawa, A]]	+	[[Category: Miyazaki T]]
-	[[Category: Tonozuka, T]]	+	[[Category: Nishikawa A]]
-	~~[[Category: Gh31]]~~	+	[[Category: Tonozuka T]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tim-barrel~~]]	+

OCA at 08:39, 5 February 2020

2020-02-05T08:39:52Z

←Older revision		Revision as of 08:39, 5 February 2020
Line 21:		Line 21:
	==See Also==		==See Also==
	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]		*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
-	*[[Galactosidase\|Galactosidase]]	+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:07, 6 June 2019

2019-06-06T00:07:52Z

←Older revision		Revision as of 00:07, 6 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with D-galactose==		==Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with D-galactose==
-	<StructureSection load='4xpp' size='340' side='right' caption='[[4xpp]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4xpp' size='340' side='right'caption='[[4xpp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ccug_39354 Ccug 39354]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xpo\|4xpo]], [[4xpq\|4xpq]], [[4xpr\|4xpr]], [[4xps\|4xps]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xpo\|4xpo]], [[4xpq\|4xpq]], [[4xpr\|4xpr]], [[4xps\|4xps]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [http://www.ebi.ac.uk/pdbsum/4xpp 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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [http://pdbe.org/4xpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [http://www.ebi.ac.uk/pdbsum/4xpp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4xpp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
		+	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-galactosidase]]		[[Category: Alpha-galactosidase]]
		+	[[Category: Ccug 39354]]
		+	[[Category: Large Structures]]
	[[Category: Ichikawa, M]]		[[Category: Ichikawa, M]]
	[[Category: Ishizaki, Y]]		[[Category: Ishizaki, Y]]

OCA at 12:11, 20 May 2015

2015-05-20T12:11:45Z

←Older revision		Revision as of 12:11, 20 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with D-galactose==
		+	<StructureSection load='4xpp' size='340' side='right' caption='[[4xpp]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xpp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xpo\|4xpo]], [[4xpq\|4xpq]], [[4xpr\|4xpr]], [[4xps\|4xps]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=4xpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xpp RCSB], [http://www.ebi.ac.uk/pdbsum/4xpp PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolase family 31 (GH31) proteins have been reportedly identified as exo-alpha-glycosidases with activity for alpha-glucosides and alpha-xylosides. We focused on a GH31 subfamily, which contains proteins with low sequence identity (<24%) to the previously reported GH31 glycosidases, and characterized two enzymes from Pedobacter heparinus and Pedobacter saltans, respectively. The enzymes unexpectedly exhibited alpha-galactosidase activity, but were not active on alpha-glucosides and alpha-xylosides. The crystal structures of one of the enzymes, PsGal31A, in unliganded form and in complexes with D-galactose or L-fucose, and the catalytic nucleophile mutant in unliganded form and in complex with p-nitrophenyl-alpha-D-galactopyranoside, were determined at 1.85-2.30 A resolution. The overall structure of PsGal31A contains four domains, and the catalytic domain adopts a (beta/alpha)8-barrel fold that resembles the structures of other GH31 enzymes. Two catalytic aspartic acid residues are structurally conserved in the enzymes, whereas most residues forming the active site differ from those of GH31 alpha-glucosidases and alpha-xylosidases. PsGal31A forms a dimer via a unique loop that is not conserved in other reported GH31 enzymes; this loop is involved in its aglycone specificity and in binding L-fucose. Considering potential genes for alpha-L-fucosidases and carbohydrate-related proteins within the vicinity of Pedobacter Gal31, the identified Gal31 enzymes are likely to function in a novel sugar degradation system. This is the first report of alpha-galactosidases which belong to GH31 family.

-	~~The entry 4xpp is ON HOLD~~	+	Structural and biochemical characterization of novel bacterial alpha-galactosidases belonging to glycoside hydrolase family 31.,Miyazaki T, Ishizaki Y, Ichikawa M, Nishikawa A, Tonozuka T Biochem J. 2015 May 5. PMID:25942325<ref>PMID:25942325</ref>

-	~~Authors: Miyazaki~~, T.~~, Ishizaki, Y~~., Ichikawa, M~~., Nishikawa, A., Tonozuka, T.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alpha-galactosidase]]
		+	[[Category: Ichikawa, M]]
		+	[[Category: Ishizaki, Y]]
		+	[[Category: Miyazaki, T]]
	[[Category: Nishikawa, A]]		[[Category: Nishikawa, A]]
-	[[Category: Ichikawa, M]]
	[[Category: Tonozuka, T]]		[[Category: Tonozuka, T]]
-	[[Category: ~~Miyazaki, T~~]]	+	[[Category: Gh31]]
-	[[Category: ~~Ishizaki, Y~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Tim-barrel]]

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

2015-01-28T15:39:53Z

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

←Older revision

Revision as of 15:39, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xpp is ON HOLD Authors: Miyazaki, T., Ishizaki, Y., Ichikawa, M., Nishikawa, A., Tonozuka, T. Description: Category: Unreleased Structures [[...

2015-01-28T15:39:52Z

New page: '''Unreleased structure''' The entry 4xpp is ON HOLD Authors: Miyazaki, T., Ishizaki, Y., Ichikawa, M., Nishikawa, A., Tonozuka, T. Description: Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 4xpp is ON HOLD

Authors: Miyazaki, T., Ishizaki, Y., Ichikawa, M., Nishikawa, A., Tonozuka, T.

Description:
[[Category: Unreleased Structures]]
[[Category: Nishikawa, A]]
[[Category: Ichikawa, M]]
[[Category: Tonozuka, T]]
[[Category: Miyazaki, T]]
[[Category: Ishizaki, Y]]