3C6M | pdb_00003c6m

Crystal structure of human spermine synthase in complex with spermine and 5-methylthioadenosine

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	KOG1562,Spermine_synt_N_1	e3c6mD1	A: beta meanders	X: Spermidine synthase tetramerisation domain (From Topology)	H: Spermidine synthase tetramerisation domain (From Topology)	T: Spermidine synthase tetramerisation domain	F: KOG1562,Spermine_synt_N_1	ECOD (1.6)
D	Spermine_synth	e3c6mD2	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_1	e3c6mC2	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_1	ECOD (1.6)
C	Spermine_synth	e3c6mC1	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_1	e3c6mB3	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_1	ECOD (1.6)
B	KOG1562	e3c6mB1	A: a+b two layers	X: TBP-like	H: S-adenosylmethionine decarboxylase-related	T: Bacterial S-adenosylmethionine decarboxylase	F: KOG1562	ECOD (1.6)
B	Spermine_synth	e3c6mB4	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)
A	Spermine_synt_N_1	e3c6mA3	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_1	ECOD (1.6)
A	KOG1562	e3c6mA1	A: a+b two layers	X: TBP-like	H: S-adenosylmethionine decarboxylase-related	T: Bacterial S-adenosylmethionine decarboxylase	F: KOG1562	ECOD (1.6)
A	Spermine_synth	e3c6mA2	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)
D	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	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)
C	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	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)
B	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	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)
A	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	CATH (4.3.0)
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)

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	PF17950	S-adenosylmethionine decarboxylase N -terminal (SpmSyn_N)	S-adenosylmethionine decarboxylase N -terminal	This is the N-terminal domain found in human spermine synthase (EC 2.5.1.22). The N-terminal domain, which forms the major part of the dimerization interface, shows a considerable structural similarity to the AdoMetDC-like fold (S-adenosylmethionine ...	This is the N-terminal domain found in human spermine synthase (EC 2.5.1.22). The N-terminal domain, which forms the major part of the dimerization interface, shows a considerable structural similarity to the AdoMetDC-like fold (S-adenosylmethionine decarboxylase, the enzyme that forms the aminopropyl donor substrate), Pfam:PF02675 . Deletion of the N-terminal domain led to a complete loss of spermine synthase activity, suggesting that dimerization may be required for activity. The N-terminal domain (amino acids 1-117) includes seven beta-strands and two alpha-helices [1].	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	Spermine synthase	spermine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	amine metabolic process metabolic process cellular process polyamine metabolic process biogenic amine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process methionine metabolic process organic acid metabolic process alpha-amino acid metabolic process small molecule metabolic process amine metabolic process metabolic process cellular process polyamine metabolic process biogenic amine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process methionine metabolic process organic acid metabolic process alpha-amino acid metabolic process small molecule metabolic process sulfur compound metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process spermine metabolic process spermine biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR040900	Spermine synthase, N-terminal	Domain
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR037163	Spermidine synthase, tetramerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR035246	Spermidine synthase, tetramerisation domain	Domain
A, B, C, D	IPR015576	Spermine synthase, animal	Family
A, B, C, D	IPR030374	Polyamine biosynthesis domain	Domain
A, B, C, D	IPR030373	Polyamine biosynthesis domain, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P52788	syndromic X-linked intellectual disability Snyder type rheumatoid arthritis intellectual disability bipolar disorder bipolar II disorder Mood Disorders

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.