4amg - Revision history

OCA at 11:30, 20 December 2023

OCA — Wed, 20 Dec 2023 11:30:13 GMT

←Older revision		Revision as of 11:30, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='4amg' size='340' side='right'caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='4amg' size='340' side='right'caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~As_4.1442 As 4.1442~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AMG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AMG FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MLY:N~~-~~DIMETHYL-LYSINE'>MLY</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]] 2.59Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[4amb\|4amb]], [[4an4\|4an4]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [https://pdbe.org/4amg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [https://www.ebi.ac.uk/pdbsum/4amg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4amg 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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [https://pdbe.org/4amg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [https://www.ebi.ac.uk/pdbsum/4amg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4amg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RN61_STRNO Q9RN61_STRNO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1442]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Claesson, M]]	+	[[Category: Streptomyces nogalater]]
-	[[Category: Dobritzsch, D]]	+	[[Category: Claesson M]]
-	[[Category: Metsa-Ketela, M]]	+	[[Category: Dobritzsch D]]
-	[[Category: Schneider, G]]	+	[[Category: Metsa-Ketela M]]
-	[[Category: Siitonen, V]]	+	[[Category: Schneider G]]
-	~~[[Category: Gt1 family]]~~	+	[[Category: Siitonen V]]
-	~~[[Category: Nogalamycin]]~~	+
-	~~[[Category: Polyketide biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:39, 25 August 2022

OCA — Thu, 25 Aug 2022 05:39:00 GMT

←Older revision		Revision as of 05:39, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='4amg' size='340' side='right'caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='4amg' size='340' side='right'caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/As_4.1442 As 4.1442]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4AMG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/As_4.1442 As 4.1442]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AMG FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4amb\|4amb]], [[4an4\|4an4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4amb\|4amb]], [[4an4\|4an4]]</div></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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [~~http~~://pdbe.org/4amg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4amg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4amg 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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [https://pdbe.org/4amg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [https://www.ebi.ac.uk/pdbsum/4amg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4amg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Glycosyltransferase\|Glycosyltransferase]]	+	*[[Glycosyltransferase 3D structures\|Glycosyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: As 4 1442]]		[[Category: As 4 1442]]
		+	[[Category: Large Structures]]
	[[Category: Claesson, M]]		[[Category: Claesson, M]]
	[[Category: Dobritzsch, D]]		[[Category: Dobritzsch, D]]

OCA at 09:26, 6 March 2019

OCA — Wed, 06 Mar 2019 09:26:25 GMT

←Older revision		Revision as of 09:26, 6 March 2019
Line 1:		Line 1:

	==Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater==		==Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater==
-	<StructureSection load='4amg' size='340' side='right' caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>	+	<StructureSection load='4amg' size='340' side='right'caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1442 As 4.1442]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AMG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1442 As 4.1442]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AMG FirstGlance]. <br>

OCA at 12:59, 11 August 2016

OCA — Thu, 11 Aug 2016 12:59:51 GMT

←Older revision		Revision as of 12:59, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater==		==Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater==
	<StructureSection load='4amg' size='340' side='right' caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='4amg' size='340' side='right' caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_nogalater Streptomyces nogalater~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AMG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1442 As 4.1442]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AMG FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4amb\|4amb]], [[4an4\|4an4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4amb\|4amb]], [[4an4\|4an4]]</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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [http://www.ebi.ac.uk/pdbsum/4amg 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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [http://pdbe.org/4amg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [http://www.ebi.ac.uk/pdbsum/4amg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4amg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4amg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces nogalater~~]]	+	[[Category: As 4 1442]]
	[[Category: Claesson, M]]		[[Category: Claesson, M]]
	[[Category: Dobritzsch, D]]		[[Category: Dobritzsch, D]]

OCA at 13:07, 4 January 2015

OCA — Sun, 04 Jan 2015 13:07:30 GMT

←Older revision		Revision as of 13:07, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~4amg.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater==
		+	<StructureSection load='4amg' size='340' side='right' caption='[[4amg]], [[Resolution\|resolution]] 2.59Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4amg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AMG FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4amb\|4amb]], [[4an4\|4an4]]</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=4amg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4amg RCSB], [http://www.ebi.ac.uk/pdbsum/4amg PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The glycosyltransferase SnogD from Streptomyces nogalater transfers a nogalamine moiety to the metabolic intermediate 3',4'-demethoxynogalose-1-hydroxynogalamycinone during the final steps of biosynthesis of the aromatic polyketide nogalamycin. The crystal structure of recombinant SnogD, as an apo-enzyme and with a bound nucleotide, 2-deoxyuridine-5'-diphosphate, was determined to 2.6 A resolution. Reductive methylation of SnogD was crucial for reproducible preparation of diffraction quality crystals due to creation of an additional intermolecular salt bridge between methylated lysine residue Lys384 and Glu374* from an adjacent molecule in the crystal lattice. SnogD is a dimer both in solution and in the crystal, and the enzyme subunit displays a fold characteristic of the GT-B family of glycosyltransferases. Binding of the nucleotide is associated with rearrangement of two active-site loops. Site-directed mutagenesis shows that two active-site histidine residues, His25 and His301, are critical for the glycosyltransferase activities of SnogD both in vivo and in vitro. The crystal structures and the functional data are consistent with a role for His301 in binding of the diphosphate group of the sugar donor substrate, and a function of His25 as a catalytic base in the glycosyl transfer reaction. Database The atomic coordinates and structure factors have been deposited with the RCSB Protein Data Bank under accession numbers 4AMB, 4AMG and 4AN4 Structured digital abstract * snogD and snogD bind by x-ray crystallography (View Interaction: 1, 2).

-	~~{{STRUCTURE_4amg\| PDB=4amg \| SCENE= }}~~	+	Crystal structure of the glycosyltransferase SnogD from the biosynthetic pathway of nogalamycin in Streptomyces nogalater.,Claesson M, Siitonen V, Dobritzsch D, Metsa-Ketela M, Schneider G FEBS J. 2012 Sep;279(17):3251-63. doi: 10.1111/j.1742-4658.2012.08711.x. Epub, 2012 Aug 17. PMID:22804797<ref>PMID:22804797</ref>

-	~~===Crystal structure~~ of the ~~glycosyltransferase SnogD from Streptomyces nogalater===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22804797}}~~	+	==See Also==
-		+	*[[Glycosyltransferase\|Glycosyltransferase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4amg~~]] ~~is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA].~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Streptomyces nogalater]]		[[Category: Streptomyces nogalater]]
-	[[Category: Claesson, M.]]	+	[[Category: Claesson, M]]
-	[[Category: Dobritzsch, D.]]	+	[[Category: Dobritzsch, D]]
-	[[Category: Metsa-Ketela, M.]]	+	[[Category: Metsa-Ketela, M]]
-	[[Category: Schneider, G.]]	+	[[Category: Schneider, G]]
-	[[Category: Siitonen, V.]]	+	[[Category: Siitonen, V]]
	[[Category: Gt1 family]]		[[Category: Gt1 family]]
	[[Category: Nogalamycin]]		[[Category: Nogalamycin]]
	[[Category: Polyketide biosynthesis]]		[[Category: Polyketide biosynthesis]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:24, 5 September 2012

OCA — Wed, 05 Sep 2012 05:24:21 GMT

←Older revision		Revision as of 05:24, 5 September 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4amg.jpg\|left\|200px]]

-	~~The entry~~ 4amg ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4amg\| PDB=4amg \| SCENE= }}

-	~~Authors: Claesson, M., Siitonen, V., Dobritzsch, D., Metsa-Ketela, M., Schneider, G.~~	+	===Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater===

-	~~Description: Crystal~~ structure ~~of the glycosyltransferase SnogD~~ from Streptomyces nogalater	+	{{ABSTRACT_PUBMED_22804797}}
		+
		+	==About this Structure==
		+	[[4amg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMG OCA].
		+	[[Category: Streptomyces nogalater]]
		+	[[Category: Claesson, M.]]
		+	[[Category: Dobritzsch, D.]]
		+	[[Category: Metsa-Ketela, M.]]
		+	[[Category: Schneider, G.]]
		+	[[Category: Siitonen, V.]]
		+	[[Category: Gt1 family]]
		+	[[Category: Nogalamycin]]
		+	[[Category: Polyketide biosynthesis]]
		+	[[Category: Transferase]]

OCA at 06:34, 11 April 2012

OCA — Wed, 11 Apr 2012 06:34:09 GMT

←Older revision		Revision as of 06:34, 11 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4amg is ON HOLD	+	The entry 4amg is ON HOLD until Paper Publication

	Authors: Claesson, M., Siitonen, V., Dobritzsch, D., Metsa-Ketela, M., Schneider, G.		Authors: Claesson, M., Siitonen, V., Dobritzsch, D., Metsa-Ketela, M., Schneider, G.

	Description: Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater		Description: Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater

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

OCA — Wed, 21 Mar 2012 07:09:21 GMT

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

←Older revision

Revision as of 07:09, 21 March 2012

OCA: New page: '''Unreleased structure''' The entry 4amg is ON HOLD Authors: Claesson, M., Siitonen, V., Dobritzsch, D., Metsa-Ketela, M., Schneider, G. Description: Crystal structure of the glycosyl...

OCA — Wed, 21 Mar 2012 07:09:20 GMT

New page: '''Unreleased structure''' The entry 4amg is ON HOLD Authors: Claesson, M., Siitonen, V., Dobritzsch, D., Metsa-Ketela, M., Schneider, G. Description: Crystal structure of the glycosyl...

New page

'''Unreleased structure'''

The entry 4amg is ON HOLD

Authors: Claesson, M., Siitonen, V., Dobritzsch, D., Metsa-Ketela, M., Schneider, G.

Description: Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater