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Structure paper

TitleThe Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.
Journal, issue, pagesJ. Mol. Biol., Vol. 432, Page 2042-2054, Year 2020
Publish dateNov 15, 2019 (structure data deposition date)
AuthorsHuang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
External linksJ. Mol. Biol. / PubMed:32061937
MethodsX-ray diffraction
Resolution1.08 - 2.1 Å
Structure data

PDB-6tge:
NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+-methenyl-H4MPT+ complex
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6tlk:
Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-6tm3:
Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in a close conformation containing NADP+ and methylene-H4MPT
Method: X-RAY DIFFRACTION / Resolution: 1.08 Å

PDB-6yk9:
[Fe]-hydrogenase from Methanolacinia paynteri with bound guanylylpyridinol at 1.7-A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6yka:
Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6ykb:
[Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP at 1.55-A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

Chemicals

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-H4M:
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-FMT:
FORMIC ACID

ChemComp-GOL:
GLYCEROL

ChemComp-CL:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-LI:
Unknown entry

ChemComp-FEG:
5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine

ChemComp-GLY:
GLYCINE

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

ChemComp-GMP:
GUANOSINE

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-FE9:
iron-guanylyl pyridinol cofactor

Source
  • methylorubrum extorquens (bacteria)
  • methylorubrum extorquens am1 (bacteria)
  • methanolacinia paynteri g-2000 (archaea)
KeywordsOXIDOREDUCTASE / dehydrogenase / tetrahydromethanotperin / NADP / methyotrophic bacteria / energy metabolism / One-carbon metabolism; Enzyme catalysis; Dehydrogenase; Conformational changes; Methylotrophy / [Fe]-hydrogenase; FeGP cofactor; guanylylpyridinol; conformational changes; GMP / [Fe]-hydrogenase; FeGP cofactor; guanylylpyridinol; asymmetry; conformational changes; GMP

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