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Structure paper

TitleThe Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates.
Journal, issue, pagesAngew. Chem. Int. Ed. Engl., Vol. 58, Page 3506-3510, Year 2019
Publish dateOct 9, 2018 (structure data deposition date)
AuthorsWatanabe, T. / Wagner, T. / Huang, G. / Kahnt, J. / Ataka, K. / Ermler, U. / Shima, S.
External linksAngew. Chem. Int. Ed. Engl. / PubMed:30600878
MethodsX-ray diffraction
Resolution1.85 - 2.5 Å
Structure data

PDB-6hux:
HmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydromethanopterin at 2.5 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-6huy:
HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form A
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-6huz:
HmdII from Desulfurobacterium thermolithotrophum reconstituted with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form B
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

Chemicals

ChemComp-ACT:
ACETATE ION

ChemComp-FE9:
iron-guanylyl pyridinol cofactor

ChemComp-NA:
Unknown entry

ChemComp-E4M:
1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol

ChemComp-MG:
Unknown entry

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-GOL:
GLYCEROL

ChemComp-GUE:
5,10-Methenyltetrahydrofolate

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

Source
  • methanocaldococcus jannaschii dsm 2661 (archaea)
  • desulfurobacterium thermolithotrophum dsm 11699 (bacteria)
KeywordsOXIDOREDUCTASE / Hydrogenase / H2-activation / Lateral gene-transfer / cofactor biosynthesis / tetrahydromethanopterin / paralog / methanogen / metalloenzyme / tetrahydrofolate / sulfur-reducing bacteria

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