6yka - Revision history

OCA at 13:29, 24 January 2024

2024-01-24T13:29:01Z

←Older revision		Revision as of 13:29, 24 January 2024
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	==Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution==		==Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution==
-	<StructureSection load='6yka' size='340' side='right'caption='[[6yka]]' scene=''>	+	<StructureSection load='6yka' size='340' side='right'caption='[[6yka]], [[Resolution\|resolution]] 2.10Å' 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=6YKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yka]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanolacinia_paynteri_G-2000 Methanolacinia paynteri G-2000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YKA 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=6yka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yka OCA], [https://pdbe.org/6yka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yka RCSB], [https://www.ebi.ac.uk/pdbsum/6yka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yka 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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6yka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yka OCA], [https://pdbe.org/6yka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yka RCSB], [https://www.ebi.ac.uk/pdbsum/6yka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yka ProSAT]</span></td></tr>
	</table>		</table>
		+	<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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yka" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Methanolacinia paynteri G-2000]]
	[[Category: Arriaza-Gallardo FJ]]		[[Category: Arriaza-Gallardo FJ]]
	[[Category: Huang G]]		[[Category: Huang G]]
	[[Category: Shima S]]		[[Category: Shima S]]
	[[Category: Wagner T]]		[[Category: Wagner T]]

OCA at 09:58, 17 February 2021

2021-02-17T09:58:30Z

←Older revision		Revision as of 09:58, 17 February 2021
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-	'''Unreleased structure'''

-	~~The entry 6yka is ON HOLD until Paper Publication~~	+	==Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution==
-		+	<StructureSection load='6yka' size='340' side='right'caption='[[6yka]]' scene=''>
-	~~Authors: Wagner, T., Huang, G., Arriaza-Gallardo, F.J., Shima, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YKA FirstGlance]. <br>
-	~~Description:~~ Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution	+	</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=6yka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yka OCA], [https://pdbe.org/6yka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yka RCSB], [https://www.ebi.ac.uk/pdbsum/6yka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yka ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Shima~~, S]]	+	__TOC__
-	[[Category: Arriaza-Gallardo~~, F.J~~]]	+	</StructureSection>
-	[[Category: ~~Wagner, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Huang, G~~]]	+	[[Category: Arriaza-Gallardo FJ]]
		+	[[Category: Huang G]]
		+	[[Category: Shima S]]
		+	[[Category: Wagner T]]

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

2020-04-15T05:33:32Z

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

←Older revision

Revision as of 05:33, 15 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yka is ON HOLD until Paper Publication Authors: Wagner, T., Huang, G., Arriaza-Gallardo, F.J., Shima, S. Description: Asymmetric [Fe]-hydrogenase ...

2020-04-15T05:33:31Z

New page: '''Unreleased structure''' The entry 6yka is ON HOLD until Paper Publication Authors: Wagner, T., Huang, G., Arriaza-Gallardo, F.J., Shima, S. Description: Asymmetric [Fe]-hydrogenase ...

New page

'''Unreleased structure'''

The entry 6yka is ON HOLD until Paper Publication

Authors: Wagner, T., Huang, G., Arriaza-Gallardo, F.J., Shima, S.

Description: Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution
[[Category: Unreleased Structures]]
[[Category: Shima, S]]
[[Category: Arriaza-Gallardo, F.J]]
[[Category: Wagner, T]]
[[Category: Huang, G]]