6tlk - Revision history

OCA at 13:04, 24 January 2024

2024-01-24T13:04:50Z

←Older revision		Revision as of 13:04, 24 January 2024
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	<StructureSection load='6tlk' size='340' side='right'caption='[[6tlk]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6tlk' size='340' side='right'caption='[[6tlk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tlk]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metea Metea~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TLK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TLK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tlk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylorubrum_extorquens_AM1 Methylorubrum extorquens AM1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TLK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.8Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtdA, MexAM1_META1p1728 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272630 METEA])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=6tlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tlk OCA], [~~http~~://pdbe.org/6tlk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tlk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tlk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tlk 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=6tlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tlk OCA], [https://pdbe.org/6tlk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tlk RCSB], [https://www.ebi.ac.uk/pdbsum/6tlk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tlk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MTDA_METEA MTDA_METEA]] Catalyzes the dehydrogenation of methylene-H(4)MPT. Can also catalyze the reversible dehydrogenation of methylene-H(4)F with 20-fold lower catalytic efficiency.	+	[https://www.uniprot.org/uniprot/MTDA_METEA MTDA_METEA] Catalyzes the dehydrogenation of methylene-H(4)MPT. Can also catalyze the reversible dehydrogenation of methylene-H(4)F with 20-fold lower catalytic efficiency.
	<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: ~~Metea~~]]	+	[[Category: Methylorubrum extorquens AM1]]
-	[[Category: Demmer, U]]	+	[[Category: Demmer U]]
-	[[Category: Ermler, U]]	+	[[Category: Ermler U]]
-	[[Category: Huang, G]]	+	[[Category: Huang G]]
-	[[Category: Shima, S]]	+	[[Category: Shima S]]
-	[[Category: Wagner, T]]	+	[[Category: Wagner T]]
-	[[Category: Warkentin, E]]	+	[[Category: Warkentin E]]
-	~~[[Category: Conformational change]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Enzyme catalysis]]~~	+
-	~~[[Category: Methylotrophy]]~~	+
-	~~[[Category: One-carbon metabolism]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:07, 20 May 2020

2020-05-20T06:07:33Z

←Older revision		Revision as of 06:07, 20 May 2020
Line 3:		Line 3:
	<StructureSection load='6tlk' size='340' side='right'caption='[[6tlk]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6tlk' size='340' side='right'caption='[[6tlk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tlk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TLK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6TLK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tlk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Metea Metea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TLK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TLK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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=6tlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tlk OCA], [http://pdbe.org/6tlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tlk RCSB], [http://www.ebi.ac.uk/pdbsum/6tlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tlk ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtdA, MexAM1_META1p1728 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272630 METEA])</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=6tlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tlk OCA], [http://pdbe.org/6tlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tlk RCSB], [http://www.ebi.ac.uk/pdbsum/6tlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tlk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Metea]]
	[[Category: Demmer, U]]		[[Category: Demmer, U]]
	[[Category: Ermler, U]]		[[Category: Ermler, U]]

OCA at 09:25, 26 February 2020

2020-02-26T09:25:16Z

←Older revision		Revision as of 09:25, 26 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tlk is ~~ON HOLD~~	+	==Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT==
		+	<StructureSection load='6tlk' size='340' side='right'caption='[[6tlk]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6tlk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TLK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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=6tlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tlk OCA], [http://pdbe.org/6tlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tlk RCSB], [http://www.ebi.ac.uk/pdbsum/6tlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tlk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MTDA_METEA MTDA_METEA]] Catalyzes the dehydrogenation of methylene-H(4)MPT. Can also catalyze the reversible dehydrogenation of methylene-H(4)F with 20-fold lower catalytic efficiency.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NADP-dependent methylene-tetrahydromethanopterin (methylene-H4MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H4MPT to form methenyl-H4MPT(+) by using NADP(+) as hydride acceptor. This hydride transfer reaction is involved in the oxidative metabolism from formaldehyde to CO2 in methylotrophic and methanotrophic bacteria. Here, we report on the crystal structures of the ternary MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in open and closed forms. Their conversion is accomplished by opening/closing the active site cleft via a 15 degrees rotation of the NADP- relative to the pterin-domain. The 1.08-A structure of the closed and active enzyme- NADP(+)-methylene-H4MPT complex allows a detailed geometric analysis of the bulky substrates and a precise prediction of the hydride trajectory. Upon domain closure, the bulky substrate rings become compressed resulting in a tilt of the imidazolidine group of methylene-H4MPT that optimizes the geometry for hydride transfer. An additional 1.5-A structure of MtdA in complex with the non-reactive NADP(+) and methenyl-H4MPT(+) revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 A, which demonstrates the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly angle of methylene-H4MPT bound to MtdA is smaller than that in the enzyme-free state but is similar to that in H2- and F420-dependent methylene-H4MPT dehydrogenases. The concept of compression-driven hydride-transfer including quantum-mechanical hydrogen-tunneling effects, which are established for flavin- and NADP-dependent enzymes, can be expanded to hydride-transferring H4MPT-dependent enzymes.

-	~~Authors: Wagner, T~~., Huang, G., ~~Demmer~~, U., Warkentin, E., Ermler, U., Shima, S.	+	The hydride transfer process in NADP dependent methylene-tetrahydromethanopterin dehydrogenase.,Huang G, Wagner T, Demmer U, Warkentin E, Ermler U, Shima S J Mol Biol. 2020 Feb 13. pii: S0022-2836(20)30108-X. doi:, 10.1016/j.jmb.2020.01.042. PMID:32061937<ref>PMID:32061937</ref>

-	~~Description: Structure~~ of ~~methylene~~-~~tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene~~-~~H4MPT~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6tlk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Demmer, U]]
		+	[[Category: Ermler, U]]
		+	[[Category: Huang, G]]
	[[Category: Shima, S]]		[[Category: Shima, S]]
	[[Category: Wagner, T]]		[[Category: Wagner, T]]
-	[[Category: Ermler, U]]
	[[Category: Warkentin, E]]		[[Category: Warkentin, E]]
-	[[Category: ~~Demmer, U~~]]	+	[[Category: Conformational change]]
-	[[Category: ~~Huang, G~~]]	+	[[Category: Dehydrogenase]]
		+	[[Category: Enzyme catalysis]]
		+	[[Category: Methylotrophy]]
		+	[[Category: One-carbon metabolism]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "6tlk" [edit=sysop:move=sysop]

2019-12-11T13:37:00Z

Protected "6tlk" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:37, 11 December 2019

OCA: New page: '''Unreleased structure''' The entry 6tlk is ON HOLD Authors: Wagner, T., Huang, G., Demmer, U., Warkentin, E., Ermler, U., Shima, S. Description: Structure of methylene-tetrahydrometh...

2019-12-11T13:36:58Z

New page: '''Unreleased structure''' The entry 6tlk is ON HOLD Authors: Wagner, T., Huang, G., Demmer, U., Warkentin, E., Ermler, U., Shima, S. Description: Structure of methylene-tetrahydrometh...

New page

'''Unreleased structure'''

The entry 6tlk is ON HOLD

Authors: Wagner, T., Huang, G., Demmer, U., Warkentin, E., Ermler, U., Shima, S.

Description: Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
[[Category: Unreleased Structures]]
[[Category: Shima, S]]
[[Category: Wagner, T]]
[[Category: Ermler, U]]
[[Category: Warkentin, E]]
[[Category: Demmer, U]]
[[Category: Huang, G]]