3HWX

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP

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)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
E [auth R]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
E [auth R]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
E [auth R]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
H [auth 1]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
H [auth 1]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
H [auth 1]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
G [auth Z]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092255	3001790	SCOP2B (2022-06-29)
G [auth Z]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8092257	3001790	SCOP2B (2022-06-29)
G [auth Z]	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092253	3001728	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)
B	TPP_enzyme_M_2	e3hwxB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
B	TPP_enzyme_C	e3hwxB2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
B	TPP_enzyme_N	e3hwxB3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
E [auth R]	TPP_enzyme_M_2	e3hwxR2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
E [auth R]	TPP_enzyme_C	e3hwxR1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
E [auth R]	TPP_enzyme_N	e3hwxR3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
F [auth S]	TPP_enzyme_M_2	e3hwxS1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
F [auth S]	TPP_enzyme_C	e3hwxS2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
F [auth S]	TPP_enzyme_N	e3hwxS3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
H [auth 1]	TPP_enzyme_M_2	e3hwx12	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
H [auth 1]	TPP_enzyme_C	e3hwx11	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
H [auth 1]	TPP_enzyme_N	e3hwx13	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
A	TPP_enzyme_M_2	e3hwxA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
A	TPP_enzyme_C	e3hwxA2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
A	TPP_enzyme_N	e3hwxA3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
C [auth I]	TPP_enzyme_M_2	e3hwxI2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
C [auth I]	TPP_enzyme_C	e3hwxI1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
C [auth I]	TPP_enzyme_N	e3hwxI3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
D [auth J]	TPP_enzyme_M_2	e3hwxJ2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
D [auth J]	TPP_enzyme_C	e3hwxJ1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
D [auth J]	TPP_enzyme_N	e3hwxJ3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
G [auth Z]	TPP_enzyme_M_2	e3hwxZ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M_2	ECOD (1.6)
G [auth Z]	TPP_enzyme_C	e3hwxZ2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
G [auth Z]	TPP_enzyme_N	e3hwxZ3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
E [auth R]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
E [auth R]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
F [auth S]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
F [auth S]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
H [auth 1]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
H [auth 1]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
C [auth I]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
C [auth I]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
D [auth J]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
D [auth J]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
G [auth Z]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
G [auth Z]	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	PF16582	Middle domain of thiamine pyrophosphate (TPP_enzyme_M_2)	Middle domain of thiamine pyrophosphate	TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by Pfam:PF00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bac ...	TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by Pfam:PF00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria [1].	Domain
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	PF02775	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	-	Domain
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	PF02776	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N)	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity transketolase or transaldolase activity transferase activity catalytic activity identical protein binding protein binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity transketolase or transaldolase activity transferase activity catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding thiamine pyrophosphate binding organic cyclic compound binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	biosynthetic process small molecule biosynthetic process ketone metabolic process menaquinone metabolic process metabolic process cellular process small molecule metabolic process menaquinone biosynthetic process ketone biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	IPR012001	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain	Domain
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	IPR004433	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase	Family
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	IPR032264	Menaquinone biosynthesis protein MenD, middle domain	Domain
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C [auth I], D [auth J], E [auth R], A, B, C [auth I], D [auth J], E [auth R], F [auth S], G [auth Z], H [auth 1]	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain