1E5Q | pdb_00001e5q

Ternary complex of saccharopine reductase from Magnaporthe grisea, NADPH and saccharopine

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d1e5qh1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
H	d1e5qh2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
G	d1e5qg1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
G	d1e5qg2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
F	d1e5qf1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
F	d1e5qf2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
E	d1e5qe1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
E	d1e5qe2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
D	d1e5qd1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
D	d1e5qd2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
C	d1e5qc1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
C	d1e5qc2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
B	d1e5qb1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
B	d1e5qb2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
A	d1e5qa1	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	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
A	d1e5qa2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Homoserine dehydrogenase-like	Saccharopine reductase	Rice blast fungus (Pyricularia grisea ) [TaxId: 148305 ],	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	8000954	3000043	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GAPDH-like	8000954	3000043	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GAPDH-like	8000954	3000043	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GAPDH-like	8000954	3000043	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8000954	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8000954	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8000954	3000043	SCOP2B (2022-06-29)
A	SCOP2 Family	Saccharopine reductase-like	8000953	4000094	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8000954	3000043	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	e1e5qH1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
H	e1e5qH2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
G	e1e5qG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
G	e1e5qG2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
F	e1e5qF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
F	e1e5qF2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
E	e1e5qE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
E	e1e5qE2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
D	e1e5qD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
D	e1e5qD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
C	e1e5qC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
C	e1e5qC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
B	e1e5qB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
B	e1e5qB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_3	F:	ECOD (20:10:01)
A	e1e5qA1	A: FwdE/GAPDH domain-like	X: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	T: Sacchrp_dh_C	F:	ECOD (20:10:01)
A	e1e5qA2	A: Rossmann-like	X: Rossmann-related	H: NAD(P)-binding Rossmann-fold domains	T:	F:	ECOD (20:10:01)

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)
H	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
G	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
F	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
E	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
D	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
C	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
B	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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)
A	1.10.1870.10	Mainly Alpha	Orthogonal Bundle	Domain 3, Saccharopine reductase	Domain 3, Saccharopine reductase	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	PF16653	Saccharopine dehydrogenase C-terminal domain (Sacchrp_dh_C)	Saccharopine dehydrogenase C-terminal domain	This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine re ...	This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF03435	Saccharopine dehydrogenase NADP binding domain (Sacchrp_dh_NADP)	Saccharopine dehydrogenase NADP binding domain	-	Family

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	Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]	saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity saccharopine dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	L-lysine biosynthetic process via aminoadipic acid lysine metabolic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-lysine biosynthetic process via aminoadipic acid lysine metabolic process oxoacid metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005097	Saccharopine dehydrogenase, NADP binding domain	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	IPR032095	Saccharopine dehydrogenase-like, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051168	Alpha-aminoadipic semialdehyde synthase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
C	saccharopine dehydrogenase (NADP+, L-glutamate-forming) M-CSA #618	Two lysine biosynthesis pathway: ubiquitous diaminopimelate pathway found in plants, bacteria and lower fungi. And the alpha-aminoadipate pathway (AAA pathway) found in higher fungi and cyanobacteria. The AAA pathway synthesises lysine from alpha-ketoglutarate and it is a member of the glutamate family of amino acid biosynthetic pathways. A number of fungi using this lysine synthesis pathway are human and plant pathogens. Selective inhibition of the essential biosynthetic pathway of lysine can be a possible means of controlling these pathogens. Saccharopine reductase catalyses the penultimate step in the AAA pathway in which glutamate and alpha-aminoadipic-delta-semialdehyde are reversibly converted to saccharophine, using, in preference, NADPH as cofactor. But it can also utilise NADH though with low catalytic efficiency.	Defined by 1 residue: ASP:C-126 \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 1.5.1.10 (PDB Primary Data)

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.

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