4AUT | pdb_00004aut

Crystal structure of the tuberculosis drug target Decaprenyl- Phosphoryl-beta-D-Ribofuranose-2-oxidoreductase (DprE1) from Mycobacterium smegmatis

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	AldO C-terminal domain-like	8045163	4004332	SCOP2 (2022-06-29)
A	SCOP2 Family	FAD-linked oxidases, N-terminal domain	8057010	4002178	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-linked oxidases C-terminal domain-like	8057009	3001317	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-binding/transporter-associated domain-like	8057011	3000913	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RNA_pol_Rpb1_3	e4autA2	A: alpha bundles	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (develop294)
A	PGDH_C	e4autA3	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: PGDH_C	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04030	D-arabinono-1,4-lactone oxidase (ALO)	D-arabinono-1,4-lactone oxidase	-	Family
A	PF01565	FAD binding domain (FAD_binding_4)	FAD binding domain	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, call ...	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE	L-gulono-1,4-lactone dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, cytochrome as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding L-gulono-1,4-lactone dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, cytochrome as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor oxidoreductase activity, acting on CH-OH group of donors D-arabinono-1,4-lactone oxidase activity	carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process cellular component organization capsule organization polysaccharide metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis capsule polysaccharide biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process cellular component organization capsule organization polysaccharide metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis capsule polysaccharide biosynthetic process external encapsulating structure organization cell wall organization or biogenesis cell wall organization response to stimulus response to chemical response to antibiotic	cellular anatomical structure membrane periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A	IPR006094	FAD linked oxidase, N-terminal	Domain
A	IPR010031	L-gulonolactone/D-arabinono-1,4-lactone oxidase-like	Family
A	IPR016166	FAD-binding domain, PCMH-type	Domain
A	IPR016171	Vanillyl-alcohol oxidase, C-terminal subdomain 2	Homologous Superfamily
A	IPR007173	D-arabinono-1,4-lactone oxidase, C-terminal domain	Domain
A	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily

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.