2RIR | pdb_00002rir

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis

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)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2B (2022-06-29)
B	SCOP2 Family	Dipicolinate synthase A chain-like	8046347	4005035	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8095910	3000044	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)
A	2-Hacid_dh_C_1	e2rirA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
A	DpaA_N	e2rirA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
B	2-Hacid_dh_C_1	e2rirB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
B	DpaA_N	e2rirB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
D	2-Hacid_dh_C_1	e2rirD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
D	DpaA_N	e2rirD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
E	2-Hacid_dh_C_1	e2rirE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
E	DpaA_N	e2rirE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
F	2-Hacid_dh_C_1	e2rirF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
F	DpaA_N	e2rirF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
G	2-Hacid_dh_C_1	e2rirG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
G	DpaA_N	e2rirG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
H	2-Hacid_dh_C_1	e2rirH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
H	DpaA_N	e2rirH2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)
C	2-Hacid_dh_C_1	e2rirC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C_1	ECOD (1.6)
C	DpaA_N	e2rirC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: DpaA_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF16924	Dipicolinate synthase subunit A N-terminal domain (DpaA_N)	Dipicolinate synthase subunit A N-terminal domain		Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF01262	Alanine dehydrogenase/PNT, C-terminal domain (AlaDh_PNT_C)	Alanine dehydrogenase/PNT, C-terminal domain	This family now also contains the lysine 2-oxoglutarate reductases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Dipicolinate synthase, A chain	oxidoreductase activity catalytic activity	sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR031629	Dipicolinate synthase subunit A, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014215	Dipicolinic acid synthetase subunit A	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR007698	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain	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.