Annotations: 9VAP

Cryo-EM structure of formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB)

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire s ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	4Fe-4S dicluster domain-containing protein	-	-	-
A	Formate dehydrogenase molybdopterin-binding subunit FdhA	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex cellular anatomical structure cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A	IPR006656	Molybdopterin oxidoreductase	Domain
A	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9VAP | pdb_00009vap

Cryo-EM structure of formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB)

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage