5euv - Revision history

OCA at 08:26, 12 July 2023

2023-07-12T08:26:30Z

←Older revision		Revision as of 08:26, 12 July 2023
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	<StructureSection load='5euv' size='340' side='right'caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5euv' size='340' side='right'caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EUV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ldr\|5ldr]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [~~http~~://pdbe.org/5euv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5euv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv 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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [https://pdbe.org/5euv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [https://www.ebi.ac.uk/pdbsum/5euv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1LZK0_9RHOB D1LZK0_9RHOB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Paracoccus sp. 32d]]		[[Category: Paracoccus sp. 32d]]
-	[[Category: Bujacz, A]]	+	[[Category: Bujacz A]]
-	[[Category: Bujacz, G]]	+	[[Category: Bujacz G]]
-	[[Category: Pietrzyk~~, A J~~]]	+	[[Category: Pietrzyk AJ]]
-	[[Category: Rutkiewicz-Krotewicz, M]]	+	[[Category: Rutkiewicz-Krotewicz M]]
-	[[Category: Sekula, B]]	+	[[Category: Sekula B]]
-	~~[[Category: Beta-d-galactosidase]]~~	+
-	~~[[Category: Cold-adapted]]~~	+
-	~~[[Category: Dimeric]]~~	+
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Glycosyl hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Native~~]]	+

OCA at 07:45, 29 April 2020

2020-04-29T07:45:55Z

←Older revision		Revision as of 07:45, 29 April 2020
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	==Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain==		==Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain==
-	<StructureSection load='5euv' size='340' side='right' caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5euv' size='340' side='right'caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EUV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ldr\|5ldr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ldr\|5ldr]]</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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [http://pdbe.org/5euv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [http://www.ebi.ac.uk/pdbsum/5euv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv 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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [http://pdbe.org/5euv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [http://www.ebi.ac.uk/pdbsum/5euv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5euv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5euv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Paracoccus sp. 32d]]		[[Category: Paracoccus sp. 32d]]
	[[Category: Bujacz, A]]		[[Category: Bujacz, A]]

OCA at 07:31, 6 December 2017

2017-12-06T07:31:40Z

←Older revision		Revision as of 07:31, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5euv' size='340' side='right' caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5euv' size='340' side='right' caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_sp._32d Paracoccus sp. 32d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EUV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ldr\|5ldr]]</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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [http://pdbe.org/5euv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [http://www.ebi.ac.uk/pdbsum/5euv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv 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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [http://pdbe.org/5euv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [http://www.ebi.ac.uk/pdbsum/5euv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of a novel dimeric beta-D-galactosidase from Paracoccus sp. 32d (ParbetaDG) was solved in space group P212121 at a resolution of 2.4 A by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric beta-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second known structure of a cold-active GH2 beta-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit. Cold-adapted beta-D-galactosidases have been the focus of extensive research owing to their utility in a variety of industrial technologies. One of their most appealing applications is in the hydrolysis of lactose, which not only results in the production of lactose-free dairy, but also eliminates the `sandy effect' and increases the sweetness of the product, thus enhancing its quality. The determined crystal structure represents the five-domain architecture of the enzyme, with its active site located in close vicinity to the dimer interface. To identify the amino-acid residues involved in the catalytic reaction and to obtain a better understanding of the mechanism of action of this atypical beta-D-galactosidase, the crystal structure in complex with galactose (ParbetaDG-Gal) was also determined. The catalytic site of the enzyme is created by amino-acid residues from the central domain 3 and from domain 4 of an adjacent monomer. The crystal structure of this dimeric beta-D-galactosidase reveals significant differences in comparison to other beta-galactosidases. The largest difference is in the fifth domain, named Bgal_windup domain 5 in ParbetaDG, which contributes to stabilization of the functional dimer. The location of this domain 5, which is unique in size and structure, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme.
		+
		+	Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d.,Rutkiewicz-Krotewicz M, Pietrzyk-Brzezinska AJ, Sekula B, Cieslinski H, Wierzbicka-Wos A, Kur J, Bujacz A Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1049-61. doi:, 10.1107/S2059798316012535. Epub 2016 Aug 31. PMID:27599737<ref>PMID:27599737</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5euv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Paracoccus sp. 32d]]
	[[Category: Bujacz, A]]		[[Category: Bujacz, A]]
	[[Category: Bujacz, G]]		[[Category: Bujacz, G]]

OCA at 15:30, 14 September 2016

2016-09-14T15:30:11Z

←Older revision		Revision as of 15:30, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5euv ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain==
-		+	<StructureSection load='5euv' size='340' side='right' caption='[[5euv]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Rutkiewicz~~-~~Krotewicz, M~~., ~~Bujacz~~, A., ~~Pietrzyk, A~~.J., ~~Sekula~~, B., ~~Bujacz~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5euv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EUV FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euv OCA], [http://pdbe.org/5euv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5euv RCSB], [http://www.ebi.ac.uk/pdbsum/5euv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5euv ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bujacz, A]]
		+	[[Category: Bujacz, G]]
		+	[[Category: Pietrzyk, A J]]
	[[Category: Rutkiewicz-Krotewicz, M]]		[[Category: Rutkiewicz-Krotewicz, M]]
-	[[Category: Bujacz, G]]
-	[[Category: Pietrzyk, A.J]]
	[[Category: Sekula, B]]		[[Category: Sekula, B]]
-	[[Category: ~~Bujacz, A~~]]	+	[[Category: Beta-d-galactosidase]]
		+	[[Category: Cold-adapted]]
		+	[[Category: Dimeric]]
		+	[[Category: Enzyme]]
		+	[[Category: Glycosyl hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Native]]

OCA at 13:54, 10 February 2016

2016-02-10T13:54:37Z

←Older revision		Revision as of 13:54, 10 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5euv is ON HOLD	+	The entry 5euv is ON HOLD until Paper Publication

	Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G.		Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G.

OCA: Protected "5euv" [edit=sysop:move=sysop]

2015-12-01T03:25:12Z

Protected "5euv" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:25, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5euv is ON HOLD Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G. Description: Crystal structure of a cold-adap...

2015-12-01T03:25:11Z

New page: '''Unreleased structure''' The entry 5euv is ON HOLD Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G. Description: Crystal structure of a cold-adap...

New page

'''Unreleased structure'''

The entry 5euv is ON HOLD

Authors: Rutkiewicz-Krotewicz, M., Bujacz, A., Pietrzyk, A.J., Sekula, B., Bujacz, G.

Description: Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain
[[Category: Unreleased Structures]]
[[Category: Rutkiewicz-Krotewicz, M]]
[[Category: Bujacz, G]]
[[Category: Pietrzyk, A.J]]
[[Category: Sekula, B]]
[[Category: Bujacz, A]]