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6tm3

From Proteopedia

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Current revision

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in a close conformation containing NADP+ and methylene-H4MPT

Structural highlights

6tm3 is a 1 chain structure with sequence from Methylorubrum extorquens AM1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.08Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6tm3"

@@ Line 3: / Line 3: @@
 <StructureSection load='6tm3' size='340' side='right'caption='[[6tm3]], [[Resolution|resolution]] 1.08&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6tm3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TM3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6tm3]] is a 1 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=6TM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TM3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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]] 1.08&#8491;</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=6tm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tm3 OCA], [http://pdbe.org/6tm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tm3 RCSB], [http://www.ebi.ac.uk/pdbsum/6tm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tm3 ProSAT]</span></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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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'>[https://proteopedia.org/fgij/fg.htm?mol=6tm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tm3 OCA], [https://pdbe.org/6tm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tm3 RCSB], [https://www.ebi.ac.uk/pdbsum/6tm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tm3 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.
+[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;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Demmer, U]]
+[[Category: Methylorubrum extorquens AM1]]
-[[Category: Ermler, U]]
+[[Category: Demmer U]]
-[[Category: Huang, G]]
+[[Category: Ermler U]]
-[[Category: Shima, S]]
+[[Category: Huang G]]
-[[Category: Wagner, T]]
+[[Category: Shima S]]
-[[Category: Warkentin, E]]
+[[Category: Wagner T]]
-[[Category: Conformational change]]
+[[Category: Warkentin E]]
-[[Category: Dehydrogenase]]
-[[Category: Enzyme catalysis]]
-[[Category: Methylotrophy]]
-[[Category: One-carbon metabolism]]
-[[Category: Oxidoreductase]]

6tm3

From Proteopedia

Current revision

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in a close conformation containing NADP+ and methylene-H4MPT

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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