2E5W

Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3

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	d2e5wa_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d2e5wb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
C	d2e5wc_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
D	d2e5wd_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Spermidine synthase	8061332	4003319	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061333	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061333	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061333	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061333	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	Spermine_synt_N	e2e5wA2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: Spermine_synt_N	ECOD (1.6)
A	Spermine_synth	e2e5wA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Spermine_synth	ECOD (1.6)
B	Spermine_synt_N	e2e5wB2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: Spermine_synt_N	ECOD (1.6)
B	Spermine_synth	e2e5wB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Spermine_synth	ECOD (1.6)
C	Spermine_synt_N	e2e5wC2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: Spermine_synt_N	ECOD (1.6)
C	Spermine_synth	e2e5wC3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Spermine_synth	ECOD (1.6)
D	Spermine_synt_N	e2e5wD2	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: Spermine_synt_N	ECOD (1.6)
D	Spermine_synth	e2e5wD3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Spermine_synth	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 (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (4.3.0)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	2.30.140.10	Mainly Beta	Roll	Spermidine Synthase	Chain: A, domain 2	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	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	Probable spermidine synthase	spermidine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	polyamine metabolic process amine metabolic process biogenic amine biosynthetic process spermidine metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process cellular process spermidine biosynthetic process biogenic amine metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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