4d7k - Revision history

OCA at 07:19, 1 May 2024

2024-05-01T07:19:11Z

←Older revision		Revision as of 07:19, 1 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_davaonensis_JCM_4913 Streptomyces davaonensis JCM 4913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_davaonensis_JCM_4913 Streptomyces davaonensis JCM 4913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D7K 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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [https://pdbe.org/4d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [https://www.ebi.ac.uk/pdbsum/4d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7k 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]] 2.22Å</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [https://pdbe.org/4d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [https://www.ebi.ac.uk/pdbsum/4d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ROSA_STRDJ ROSA_STRDJ]] Catalyzes the S-adenosyl methionine-dependent conversion of 8-amino-8-demethyl-D-riboflavin (AF) into 8-methylamino-8-demethyl-D-riboflavin (MAF) and roseoflavin (RoF), the last two steps in the biosynthesis of the antibiotic roseoflavin.<ref>PMID:21911488</ref> <ref>PMID:26913589</ref>	+	[https://www.uniprot.org/uniprot/ROSA_STRDJ ROSA_STRDJ] Catalyzes the S-adenosyl methionine-dependent conversion of 8-amino-8-demethyl-D-riboflavin (AF) into 8-methylamino-8-demethyl-D-riboflavin (MAF) and roseoflavin (RoF), the last two steps in the biosynthesis of the antibiotic roseoflavin.<ref>PMID:21911488</ref> <ref>PMID:26913589</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	N,N-8-demethyl-8-amino-D-riboflavin dimethyltransferase (RosA) catalyzes the final dimethylation of 8-demethyl-8-amino-D-riboflavin (AF) to the antibiotic roseoflavin (RoF) in Streptomyces davawensis. In the present study we have solved the X-ray structure of RosA and determined the binding properties of substrates and products. Moreover, we have used steady-state and rapid reaction kinetics to obtain detailed information on the reaction mechanism. The structure of RosA was found to be similar to previously determined S-adenosylmethionine (SAM)-dependent methyltransferases featuring two domains, a mainly alpha-helical "orthogonal bundle" and a Rossmann-like domain (alpha/beta twisted open-sheet). Bioinformatics and molecular modelling enabled us to predict the potential SAM and AF binding sites in RosA suggesting that both substrates, AF and SAM, can bind independently to their respective binding pocket. This was confirmed by kinetic experiments that demonstrated a random-order bi-bi reaction mechanism. Furthermore, we have determined the dissociation constants for substrates and products by either isothermal titration calorimetry or UV-Vis absorption spectroscopy. This revealed that both products, RoF and S-adenosylhomocysteine (SAH), bind more tightly to RosA when compared to the substrates, AF and SAM. This suggests that RosA may contribute to roseoflavin resistance in S. davawensis. The tighter binding of products is also reflected by inhibition experiments, i.e. RoF and SAH behave as competitive inhibitors for AF and SAM, respectively. We could also show that formation of a ternary complex of RosA, RoF and SAH (or SAM) leads to drastic spectral changes that are indicative of a hydrophobic environment. This article is protected by copyright. All rights reserved.	+
-		+
-	Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-D-riboflavin to the antibiotic roseoflavin.,Tongsook C, Uhl MK, Jankowitsch F, Mack M, Gruber K, Macheroux P FEBS J. 2016 Feb 23. doi: 10.1111/febs.13690. PMID:26913589<ref>PMID:26913589</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4d7k" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:51, 14 September 2022

2022-09-14T07:51:05Z

←Older revision		Revision as of 07:51, 14 September 2022
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	<StructureSection load='4d7k' size='340' side='right'caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>		<StructureSection load='4d7k' size='340' side='right'caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strdj Strdj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_davaonensis_JCM_4913 Streptomyces davaonensis JCM 4913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D7K FirstGlance]. <br>
-	</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [~~http~~://pdbe.org/4d7k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d7k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7k ProSAT]</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [https://pdbe.org/4d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [https://www.ebi.ac.uk/pdbsum/4d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/ROSA_STRDJ ROSA_STRDJ]] Catalyzes the S-adenosyl methionine-dependent conversion of 8-amino-8-demethyl-D-riboflavin (AF) into 8-methylamino-8-demethyl-D-riboflavin (MAF) and roseoflavin (RoF), the last two steps in the biosynthesis of the antibiotic roseoflavin.<ref>PMID:21911488</ref> <ref>PMID:26913589</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Strdj~~]]	+	[[Category: Streptomyces davaonensis JCM 4913]]
-	[[Category: Gruber, K]]	+	[[Category: Gruber K]]
-	[[Category: Uhl~~, M K]]~~	+	[[Category: Uhl MK]]
-	~~[[Category: Alpha/beta twisted open-sheet]]~~	+
-	~~[[Category: Flavin]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Riboflavin]]~~	+
-	~~[[Category: Roseoflavin biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:36, 27 March 2019

2019-03-27T07:36:46Z

←Older revision		Revision as of 07:36, 27 March 2019
Line 1:		Line 1:

	==Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis==		==Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis==
-	<StructureSection load='4d7k' size='340' side='right' caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>	+	<StructureSection load='4d7k' size='340' side='right'caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Strdj Strdj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D7K FirstGlance]. <br>
-	</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [http://pdbe.org/4d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [http://www.ebi.ac.uk/pdbsum/4d7k PDBsum]</span></td></tr>	+	</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [http://pdbe.org/4d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [http://www.ebi.ac.uk/pdbsum/4d7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Strdj]]
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
	[[Category: Uhl, M K]]		[[Category: Uhl, M K]]

OCA at 19:39, 9 March 2016

2016-03-09T19:39:44Z

←Older revision		Revision as of 19:39, 9 March 2016
Line 6:		Line 6:
	</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [http://pdbe.org/4d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [http://www.ebi.ac.uk/pdbsum/4d7k PDBsum]</span></td></tr>		</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [http://pdbe.org/4d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [http://www.ebi.ac.uk/pdbsum/4d7k PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N,N-8-demethyl-8-amino-D-riboflavin dimethyltransferase (RosA) catalyzes the final dimethylation of 8-demethyl-8-amino-D-riboflavin (AF) to the antibiotic roseoflavin (RoF) in Streptomyces davawensis. In the present study we have solved the X-ray structure of RosA and determined the binding properties of substrates and products. Moreover, we have used steady-state and rapid reaction kinetics to obtain detailed information on the reaction mechanism. The structure of RosA was found to be similar to previously determined S-adenosylmethionine (SAM)-dependent methyltransferases featuring two domains, a mainly alpha-helical "orthogonal bundle" and a Rossmann-like domain (alpha/beta twisted open-sheet). Bioinformatics and molecular modelling enabled us to predict the potential SAM and AF binding sites in RosA suggesting that both substrates, AF and SAM, can bind independently to their respective binding pocket. This was confirmed by kinetic experiments that demonstrated a random-order bi-bi reaction mechanism. Furthermore, we have determined the dissociation constants for substrates and products by either isothermal titration calorimetry or UV-Vis absorption spectroscopy. This revealed that both products, RoF and S-adenosylhomocysteine (SAH), bind more tightly to RosA when compared to the substrates, AF and SAM. This suggests that RosA may contribute to roseoflavin resistance in S. davawensis. The tighter binding of products is also reflected by inhibition experiments, i.e. RoF and SAH behave as competitive inhibitors for AF and SAM, respectively. We could also show that formation of a ternary complex of RosA, RoF and SAH (or SAM) leads to drastic spectral changes that are indicative of a hydrophobic environment. This article is protected by copyright. All rights reserved.
		+
		+	Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-D-riboflavin to the antibiotic roseoflavin.,Tongsook C, Uhl MK, Jankowitsch F, Mack M, Gruber K, Macheroux P FEBS J. 2016 Feb 23. doi: 10.1111/febs.13690. PMID:26913589<ref>PMID:26913589</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4d7k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:47, 2 March 2016

2016-03-02T06:47:35Z

←Older revision		Revision as of 06:47, 2 March 2016
Line 1:		Line 1:
		+
	==Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis==		==Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis==
	<StructureSection load='4d7k' size='340' side='right' caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>		<StructureSection load='4d7k' size='340' side='right' caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>

OCA at 20:18, 13 January 2016

2016-01-13T20:18:42Z

←Older revision		Revision as of 20:18, 13 January 2016
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis==
-		+	<StructureSection load='4d7k' size='340' side='right' caption='[[4d7k]], [[Resolution\|resolution]] 2.22Å' scene=''>
-	~~The entry 4d7k is ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4d7k]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D7K FirstGlance]. <br>
-	~~Authors: Uhl, M.K., Gruber, K.~~	+	</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=4d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7k OCA], [http://pdbe.org/4d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7k RCSB], [http://www.ebi.ac.uk/pdbsum/4d7k PDBsum]</span></td></tr>
-		+	</table>
-	~~Description:~~ Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis	+	__TOC__
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</StructureSection>
-	[[~~Category~~: ~~Uhl~~, M.K]]	+
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
		+	[[Category: Uhl, M K]]
		+	[[Category: Alpha/beta twisted open-sheet]]
		+	[[Category: Flavin]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Riboflavin]]
		+	[[Category: Roseoflavin biosynthesis]]
		+	[[Category: Transferase]]

OCA at 13:57, 24 December 2014

2014-12-24T13:57:17Z

←Older revision		Revision as of 13:57, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis		Description: Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis
		+	[[Category: Unreleased Structures]]
		+	[[Category: Uhl, M.K]]
		+	[[Category: Gruber, K]]

OCA: Protected "4d7k" [edit=sysop:move=sysop]

2014-12-03T08:02:15Z

Protected "4d7k" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:02, 3 December 2014

OCA: New page: '''Unreleased structure''' The entry 4d7k is ON HOLD until Paper Publication Authors: Uhl, M.K., Gruber, K. Description: Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimeth...

2014-12-03T08:02:13Z

New page: '''Unreleased structure''' The entry 4d7k is ON HOLD until Paper Publication Authors: Uhl, M.K., Gruber, K. Description: Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimeth...

New page

'''Unreleased structure'''

The entry 4d7k is ON HOLD until Paper Publication

Authors: Uhl, M.K., Gruber, K.

Description: Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis