7p8m - Revision history

OCA at 13:02, 1 February 2024

OCA — Thu, 01 Feb 2024 13:02:26 GMT

←Older revision		Revision as of 13:02, 1 February 2024
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	<StructureSection load='7p8m' size='340' side='right'caption='[[7p8m]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='7p8m' size='340' side='right'caption='[[7p8m]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7p8m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P8M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p8m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P8M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PO:TRIPHOSPHATE'>3PO</scene>, <scene name='pdbligand=6IH:4,5-dimethoxy-2-nitro+benzyme+S-adenosyl-methionine'>6IH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.71Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methionine_adenosyltransferase Methionine adenosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.6 2.5.1.6] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PO:TRIPHOSPHATE'>3PO</scene>, <scene name='pdbligand=6IH:4,5-dimethoxy-2-nitro+benzyme+S-adenosyl-methionine'>6IH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7p8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p8m OCA], [https://pdbe.org/7p8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p8m RCSB], [https://www.ebi.ac.uk/pdbsum/7p8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p8m 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=7p8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p8m OCA], [https://pdbe.org/7p8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p8m RCSB], [https://www.ebi.ac.uk/pdbsum/7p8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p8m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/METK_METJA METK_METJA]] Catalyzes the formation of S-adenosylmethionine from methionine and ATP.<ref>PMID:10660563</ref>	+	[https://www.uniprot.org/uniprot/METK_METJA METK_METJA] Catalyzes the formation of S-adenosylmethionine from methionine and ATP.<ref>PMID:10660563</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7p8m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7p8m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[S-adenosylmethionine synthetase 3D structures\|S-adenosylmethionine synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Methionine adenosyltransferase~~]]	+	[[Category: Methanocaldococcus jannaschii DSM 2661]]
-	[[Category: Cornelissen~~, N V~~]]	+	[[Category: Cornelissen NV]]
-	[[Category: Herrmann, E]]	+	[[Category: Herrmann E]]
-	[[Category: Kuemmel, D]]	+	[[Category: Kuemmel D]]
-	[[Category: Peters, A]]	+	[[Category: Peters A]]
-	[[Category: Rentmeister, A]]	+	[[Category: Rentmeister A]]
-	~~[[Category: Transferase~~]]	+

OCA at 07:40, 19 January 2022

OCA — Wed, 19 Jan 2022 07:40:46 GMT

←Older revision		Revision as of 07:40, 19 January 2022
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	==Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii in complex with DMNB-SAM (4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine)==		==Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii in complex with DMNB-SAM (4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine)==
-	<StructureSection load='7p8m' size='340' side='right'caption='[[7p8m]]' scene=''>	+	<StructureSection load='7p8m' size='340' side='right'caption='[[7p8m]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P8M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p8m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P8M 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=7p8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p8m OCA], [https://pdbe.org/7p8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p8m RCSB], [https://www.ebi.ac.uk/pdbsum/7p8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p8m ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PO:TRIPHOSPHATE'>3PO</scene>, <scene name='pdbligand=6IH:4,5-dimethoxy-2-nitro+benzyme+S-adenosyl-methionine'>6IH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methionine_adenosyltransferase Methionine adenosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.6 2.5.1.6] </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=7p8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p8m OCA], [https://pdbe.org/7p8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p8m RCSB], [https://www.ebi.ac.uk/pdbsum/7p8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p8m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/METK_METJA METK_METJA]] Catalyzes the formation of S-adenosylmethionine from methionine and ATP.<ref>PMID:10660563</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo-cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non-damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non-natural groups, including first evidence for accepting photo-cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC-MjMAT) is 308-fold more efficient at converting ortho-nitrobenzyl-(ONB)-homocysteine than the wildtype enzyme. PC-MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC-MjMAT in complex with AdoONB and a red-shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC-MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC-MjMAT exhibits remarkable activity on methionine analogues with red-shifted ONB-derivatives enabling photo-deprotection of modified DNA by visible light.
		+
		+	Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases.,Peters A, Herrmann E, Cornelissen NV, Klocker N, Kummel D, Rentmeister A Chembiochem. 2021 Oct 4. doi: 10.1002/cbic.202100437. PMID:34606675<ref>PMID:34606675</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7p8m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cornelissen NV]]	+	[[Category: Methionine adenosyltransferase]]
-	[[Category: Herrmann E]]	+	[[Category: Cornelissen, N V]]
-	[[Category: Kuemmel D]]	+	[[Category: Herrmann, E]]
-	[[Category: Peters A]]	+	[[Category: Kuemmel, D]]
-	[[Category: Rentmeister A]]	+	[[Category: Peters, A]]
		+	[[Category: Rentmeister, A]]
		+	[[Category: Transferase]]

OCA at 13:38, 17 November 2021

OCA — Wed, 17 Nov 2021 13:38:34 GMT

←Older revision		Revision as of 13:38, 17 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7p8m is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii in complex with DMNB-SAM (4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine)==
-		+	<StructureSection load='7p8m' size='340' side='right'caption='[[7p8m]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P8M FirstGlance]. <br>
-	~~Description~~:	+	</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=7p8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p8m OCA], [https://pdbe.org/7p8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p8m RCSB], [https://www.ebi.ac.uk/pdbsum/7p8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p8m ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cornelissen NV]]
		+	[[Category: Herrmann E]]
		+	[[Category: Kuemmel D]]
		+	[[Category: Peters A]]
		+	[[Category: Rentmeister A]]

OCA at 07:26, 8 September 2021

OCA — Wed, 08 Sep 2021 07:26:53 GMT

←Older revision		Revision as of 07:26, 8 September 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7p8m is ON HOLD	+	The entry 7p8m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7p8m" [edit=sysop:move=sysop]

OCA — Wed, 28 Jul 2021 09:33:09 GMT

Protected "7p8m" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:33, 28 July 2021

OCA: New page: '''Unreleased structure''' The entry 7p8m is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 28 Jul 2021 09:33:08 GMT

New page: '''Unreleased structure''' The entry 7p8m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7p8m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]