6TGV | pdb_00006tgv

Crystal structure of Mycobacterium smegmatis CoaBC in complex with CTP and FMN

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	SCOP2B Superfamily	CoaB-like	8075790	3001036	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CoaB-like	8075790	3001036	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CoaB-like	8075790	3001036	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CoaB-like	8075790	3001036	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	DFP	e6tgvD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DFP	ECOD (1.6)
D	Flavoprotein	e6tgvD2	A: a/b three-layered sandwiches	X: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	H: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	T: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	F: Flavoprotein	ECOD (1.6)
C	DFP	e6tgvC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DFP	ECOD (1.6)
C	Flavoprotein	e6tgvC2	A: a/b three-layered sandwiches	X: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	H: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	T: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	F: Flavoprotein	ECOD (1.6)
B	DFP	e6tgvB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DFP	ECOD (1.6)
B	Flavoprotein	e6tgvB2	A: a/b three-layered sandwiches	X: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	H: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	T: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	F: Flavoprotein	ECOD (1.6)
A	DFP	e6tgvA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DFP	ECOD (1.6)
A	Flavoprotein	e6tgvA2	A: a/b three-layered sandwiches	X: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	H: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD (From Topology)	T: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	F: Flavoprotein	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1950	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavin prenyltransferase-like	CATH (utative)
D	3.40.50.10300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CoaB-like	CATH (utative)
C	3.40.50.1950	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavin prenyltransferase-like	CATH (utative)
C	3.40.50.10300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CoaB-like	CATH (utative)
B	3.40.50.1950	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavin prenyltransferase-like	CATH (utative)
B	3.40.50.10300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CoaB-like	CATH (utative)
A	3.40.50.1950	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavin prenyltransferase-like	CATH (utative)
A	3.40.50.10300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CoaB-like	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02441	Flavoprotein (Flavoprotein)	Flavoprotein	This domain is found in diverse flavoprotein enzymes, including covering the whole length of the sequence of epidermin biosynthesis protein from Staphylococcus epidermidis (EpiD, Swiss:P30197), which has been shown to bind FMN [1]. This enzyme cataly ...	This domain is found in diverse flavoprotein enzymes, including covering the whole length of the sequence of epidermin biosynthesis protein from Staphylococcus epidermidis (EpiD, Swiss:P30197), which has been shown to bind FMN [1]. This enzyme catalyses the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance [2]. dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase Swiss:P33751 (EC:4.1.1.-) [3].	Domain
A, B, C, D	PF04127	DNA/pantothenate metabolism flavoprotein C-terminal domain (DFP)	DNA/pantothenate metabolism flavoprotein C-terminal domain	The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism. This entry represents the C-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Coenzyme A biosynthesis bifunctional protein CoaBC	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding acid-amino acid ligase activity phosphopantothenate--cysteine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding acid-amino acid ligase activity phosphopantothenate--cysteine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity phosphopantothenoylcysteine decarboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity cation binding metal ion binding	catabolic process pantothenate metabolic process oxoacid metabolic process modified amino acid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process modified amino acid catabolic process vitamin catabolic process vitamin metabolic process water-soluble vitamin catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process metabolic process catabolic process pantothenate metabolic process oxoacid metabolic process modified amino acid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process modified amino acid catabolic process vitamin catabolic process vitamin metabolic process water-soluble vitamin catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process amide metabolic process monocarboxylic acid metabolic process pantothenate catabolic process small molecule catabolic process nucleoside phosphate metabolic process coenzyme A biosynthetic process amide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process sulfur compound metabolic process phosphorus metabolic process coenzyme A metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm phosphopantothenoylcysteine decarboxylase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036551	Flavin prenyltransferase-like	Homologous Superfamily
A, B, C, D	IPR005252	Coenzyme A biosynthesis bifunctional protein CoaBC	Family
A, B, C, D	IPR007085	DNA/pantothenate metabolism flavoprotein, C-terminal	Domain
A, B, C, D	IPR035929	CoaB-like superfamily	Homologous Superfamily
A, B, C, D	IPR003382	Flavoprotein	Domain

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.