4YV0

Crystal structure of Trypanosoma cruzi spermidine synthase in complex with (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine- 2-carboxamid

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)
C	d4yv0c_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Trypanosoma cruzi strain CL Brener ) [TaxId: 353153 ],	SCOPe (2.08)
D	d4yv0d_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Trypanosoma cruzi strain CL Brener ) [TaxId: 353153 ],	SCOPe (2.08)
A	d4yv0a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Trypanosoma cruzi strain CL Brener ) [TaxId: 353153 ],	SCOPe (2.08)
B	d4yv0b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Trypanosoma cruzi strain CL Brener ) [TaxId: 353153 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061329	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061329	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061329	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8061329	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)
C	Spermine_synt_N	e4yv0C2	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	e4yv0C1	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	e4yv0D1	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	e4yv0D2	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	e4yv0A2	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	e4yv0A1	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	e4yv0B2	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	e4yv0B1	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)
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)
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, 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	Spermidine synthase, putative	spermidine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process polyamine metabolic process biogenic amine metabolic process	-

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.