1YL7 | pdb_00001yl7

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d1yl7h1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
H	d1yl7h2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
H	d1yl7h3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
G	d1yl7g1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
G	d1yl7g2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
G	d1yl7g3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
F	d1yl7f1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
F	d1yl7f2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
F	d1yl7f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E	d1yl7e1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E	d1yl7e2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E	d1yl7e3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1yl7d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1yl7d2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1yl7d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1yl7c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1yl7c2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1yl7c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1yl7b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1yl7b2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1yl7b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1yl7a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1yl7a2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1yl7a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8058142	3000043	SCOP2B (2022-06-29)
A	SCOP2 Family	Dihydrodipicolinate reductase-like	8058141	4000095	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8058142	3000043	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)
H	YceM-like_C	e1yl7H1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
H	NAD_binding_3	e1yl7H2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
G	YceM-like_C	e1yl7G1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
G	NAD_binding_3	e1yl7G2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
F	YceM-like_C	e1yl7F1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
F	NAD_binding_3	e1yl7F2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
E	YceM-like_C	e1yl7E1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
E	NAD_binding_3	e1yl7E2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
D	YceM-like_C	e1yl7D1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
D	NAD_binding_3	e1yl7D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
C	YceM-like_C	e1yl7C1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
C	NAD_binding_3	e1yl7C2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
B	YceM-like_C	e1yl7B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
B	NAD_binding_3	e1yl7B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (develop294)
A	DapB_C	e1yl7A1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (develop294)
A	DapB_N	e1yl7A2	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
G	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
F	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
E	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
C	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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	PF05173	Dihydrodipicolinate reductase, C-terminus (DapB_C)	Dihydrodipicolinate reductase, C-terminus	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for bot ...	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF01113	Dihydrodipicolinate reductase, N-terminus (DapB_N)	Dihydrodipicolinate reductase, N-terminus	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for bo ...	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.	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	Dihydrodipicolinate reductase	NAD binding NADH binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NADPH binding NADP binding oxidoreductase activity NAD binding NADH binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NADPH binding NADP binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor 4-hydroxy-tetrahydrodipicolinate reductase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor	diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process dicarboxylic acid biosynthetic process lipid metabolic process lysine metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process alpha-amino acid metabolic process L-lysine biosynthetic process via diaminopimelate L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000846	Dihydrodipicolinate reductase, N-terminal	Domain
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	IPR022663	Dihydrodipicolinate reductase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023940	Dihydrodipicolinate reductase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022664	Dihydrodipicolinate reductase, conserved site	Conserved Site