3C6K | pdb_00003c6k

Crystal structure of human spermine synthase in complex with spermidine 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	Acyl-CoA_dh_M	e3c6kD5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acyl-CoA_dh_M	ECOD (v294.1)
D	SAM_KSR1_N	e3c6kD2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
C	Acyl-CoA_dh_M	e3c6kC5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acyl-CoA_dh_M	ECOD (v294.1)
C	Glycos_transf_1	e3c6kC3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Glycos_transf_1	ECOD (v294.1)
C	p450	e3c6kC4	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: p450	ECOD (v294.1)
B	Acyl-CoA_dh_M	e3c6kB5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acyl-CoA_dh_M	ECOD (v294.1)
B	SAM_KSR1_N	e3c6kB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
A	HTH_24	e3c6kA5	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (v294.1)
A	SAM_KSR1_N	e3c6kA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)

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 L-methionine metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid 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 L-methionine metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic 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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.