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Structure paper

TitleSubstrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement.
Journal, issue, pagesChem Sci, Vol. 15, Page 13090-13101, Year 2024
Publish dateDec 6, 2023 (structure data deposition date)
AuthorsVilela-Alves, G. / Manuel, R.R. / Viegas, A. / Carpentier, P. / Biaso, F. / Guigliarelli, B. / Pereira, I.A.C. / Romao, M.J. / Mota, C.
External linksChem Sci / PubMed:39148770
MethodsX-ray diffraction
Resolution1.664 - 2.301 Å
Structure data

PDB-8rc8:
W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 0 min
Method: X-RAY DIFFRACTION / Resolution: 2.005 Å

PDB-8rc9:
W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 2 h
Method: X-RAY DIFFRACTION / Resolution: 2.06 Å

PDB-8rca:
W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 1 h in the absence of Formate
Method: X-RAY DIFFRACTION / Resolution: 1.664 Å

PDB-8rcb:
W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air (in a not degassed drop) for 34 min in the presence of Formate
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-8rcc:
W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soaked with 48 bar CO2 for 1 min
Method: X-RAY DIFFRACTION / Resolution: 2.301 Å

Chemicals

ChemComp-MGD:
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-W:
Unknown entry

ChemComp-H2S:
HYDROSULFURIC ACID

ChemComp-GOL:
GLYCEROL

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

ChemComp-OXY:
OXYGEN MOLECULE

ChemComp-CO2:
CARBON DIOXIDE

Source
  • desulfovibrio vulgaris str. hildenborough (bacteria)
  • nitratidesulfovibrio vulgaris str. hildenborough (bacteria)
KeywordsOXIDOREDUCTASE / Formate / CO2 / Molybdenum and Tungsten enzymes / DMSO reductase family / ELECTRON TRANSPORT

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