4YLF | pdb_00004ylf

Insights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase structure

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	IL8	e4ylfD1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: Ribosomal protein S7	T: Ribosomal protein S7	F: IL8	ECOD (v294.1)
B	IL8	e4ylfB1	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: Ribosomal protein S7	T: Ribosomal protein S7	F: IL8	ECOD (v294.1)
C	Glyco_hydro_31_3rd	e4ylfC1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	ECOD (v294.1)
A	PAP_assoc	e4ylfA1	A: a/b three-layered sandwiches	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: PAP_assoc	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
B, D	PF14691	Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster (Fer4_20)	Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster	Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This doma ...	Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This domain carries two Fe4-S4 clusters.	Domain
A, C	PF10418	Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B (DHODB_Fe-S_bind)	Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B	Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B [1]. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a ...	Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B [1]. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localised in a well-ordered part of this domain close to the FAD binding site [1]. The FAD and and NAD binding domains are FAD_binding_6, Pfam:PF00970 and NAD_binding_1, Pfam:PF00175.	Domain
A, C	PF00175	Oxidoreductase NAD-binding domain (NAD_binding_1)	Oxidoreductase NAD-binding domain	Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.	Domain
A, C	PF00970	Oxidoreductase FAD-binding domain (FAD_binding_6)	Oxidoreductase FAD-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Dihydropyrimidine dehydrogenase subunit A	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding cation binding ion binding metal ion binding	-	-
A, C	Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding cation binding oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding cation binding metal ion binding	nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process nucleotide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process nucleotide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process pyrimidine nucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR028261	Dihydroprymidine dehydrogenase domain II	Domain
B, D	IPR023753	FAD/NAD(P)-binding domain	Domain
B, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
B, D	IPR006004	Sulfide dehydrogenase subunit alpha-like	Family
B, D	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
A, C	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
A, C	IPR019480	Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain	Domain
A, C	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
A, C	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain	Domain
A, C	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
A, C	IPR050353	Dihydroorotate dehydrogenase B electron transfer subunit	Family
A, C	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
A, C	IPR012165	Cytochrome-c3 hydrogenase, gamma subunit	Family

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.