6O65

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) in complex with decarboxylated S-adenosylmethionine and cyclohexylamine

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)
A	d6o65a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6o65b1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6o65b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6o65c_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d6o65d1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d6o65d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d6o65e_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d6o65f1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d6o65f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
G	d6o65g_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
H	d6o65h1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	Spermidine synthase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
H	d6o65h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043941	3000118	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	PF17284	e6o65A1	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
A	PF01564	e6o65A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
B	PF17284	e6o65B1	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
B	PF01564	e6o65B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
C	PF17284	e6o65C1	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
C	PF01564	e6o65C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
D	PF17284	e6o65D1	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
D	PF01564	e6o65D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
E	PF17284	e6o65E2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
E	PF01564	e6o65E1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
F	PF17284	e6o65F2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
F	PF01564	e6o65F1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
G	PF17284	e6o65G2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
G	PF01564	e6o65G1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)
H	PF17284	e6o65H1	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: PF17284	ECOD (1.6)
H	PF01564	e6o65H2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01564	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
B	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
C	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
D	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
E	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
E	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
F	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
F	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
G	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
G	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
H	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (utative)
H	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)

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	PF17284	Spermidine synthase tetramerisation domain (Spermine_synt_N)	Spermidine synthase tetramerisation domain	This domain represents the N-terminal tetramerization domain from spermidine synthase.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF01564	Spermine/spermidine synthase domain (Spermine_synth)	Spermine/spermidine synthase domain	Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyses the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase.	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	Spermidine synthase 1	spermidine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	organonitrogen compound metabolic process organonitrogen compound biosynthetic process polyamine metabolic process amine metabolic process biogenic amine biosynthetic process spermidine metabolic process organic substance metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process organic substance biosynthetic process metabolic process spermidine biosynthetic process biogenic amine metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR030668	Spermidine/spermine synthase, eukaryotes	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001045	Spermidine/spermine synthases	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR030374	Polyamine biosynthesis domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR037163	Spermidine synthase, tetramerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR030373	Polyamine biosynthesis domain, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035246	Spermidine synthase, tetramerisation domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.