3RW9

Crystal Structure of human Spermidine Synthase in Complex with decarboxylated S-adenosylhomocysteine

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3rw9a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rw9b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Spermidine synthase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	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	8043378	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8043378	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	e3rw9A3	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	e3rw9A2	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	e3rw9B3	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	e3rw9B2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	Spermidine synthase	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity spermidine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	amine metabolic process biogenic amine biosynthetic process spermidine metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process spermidine biosynthetic process polyamine metabolic process biogenic amine metabolic process response to peptide response to stimulus response to chemical response to cytokine amine metabolic process biogenic amine biosynthetic process spermidine metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process spermidine biosynthetic process polyamine metabolic process biogenic amine metabolic process response to peptide response to stimulus response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P19623	Adenocarcinoma of Lung Ewing sarcoma lung adenocarcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis androgenetic alopecia interstitial cystitis lung cancer pancreatic intraductal papillary-mucinous carcinoma psoriasis large cell medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome

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.