1VR7

Crystal structure of S-adenosylmethionine decarboxylase proenzyme (TM0655) from THERMOTOGA MARITIMA at 1.2 A resolution

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vr7a_	Alpha and beta proteins (a+b)	S-adenosylmethionine decarboxylase	S-adenosylmethionine decarboxylase	Bacterial S-adenosylmethionine decarboxylase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vr7b_	Alpha and beta proteins (a+b)	S-adenosylmethionine decarboxylase	S-adenosylmethionine decarboxylase	Bacterial S-adenosylmethionine decarboxylase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Bacterial S-adenosylmethionine decarboxylase	8020316	4002834	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosylmethionine decarboxylase	8032696	3001051	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosylmethionine decarboxylase	8032696	3001051	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	AdoMet_dc	e1vr7A1	A: a+b two layers	X: TBP-like	H: S-adenosylmethionine decarboxylase-related	T: Bacterial S-adenosylmethionine decarboxylase	F: AdoMet_dc	ECOD (1.6)
B	AdoMet_dc	e1vr7B2	A: a+b two layers	X: TBP-like	H: S-adenosylmethionine decarboxylase-related	T: Bacterial S-adenosylmethionine decarboxylase	F: AdoMet_dc	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.90.10	Alpha Beta	4-Layer Sandwich	S-adenosylmethionine decarboxylase	S-adenosylmethionine decarboxylase	CATH (4.3.0)
B	3.60.90.10	Alpha Beta	4-Layer Sandwich	S-adenosylmethionine decarboxylase	S-adenosylmethionine decarboxylase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02675	S-adenosylmethionine decarboxylase (AdoMet_dc)	S-adenosylmethionine decarboxylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	S-adenosylmethionine decarboxylase proenzyme	adenosylmethionine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	organonitrogen compound metabolic process organonitrogen compound biosynthetic process polyamine metabolic process amine metabolic process biogenic amine biosynthetic process spermidine metabolic process organic substance metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process organic substance biosynthetic process metabolic process spermidine biosynthetic process biogenic amine metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016067	S-adenosylmethionine decarboxylase, core	Homologous Superfamily
A, B	IPR042284	S-adenosylmethionine decarboxylase, N-terminal	Homologous Superfamily
A, B	IPR017716	S-adenosylmethionine decarboxylase proenzyme	Family
A, B	IPR003826	S-adenosylmethionine decarboxylase family, prokaryotic	Family
A, B	IPR042286	S-adenosylmethionine decarboxylase, C-terminal	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	adenosylmethionine decarboxylase (prokaryotic) M-CSA #225	S-adenosylmethionine decarboxylase (AdoMetDC) isolated from Thermotoga maritima is an enzyme that catalyses the decarboxylation of S-adenosylmethionine (AdoMet or SAM) to S-adenosyl-5'-(3-methylthiopropylamine) (dcAdoMet). AdoMetDC is regulatory enzyme in the biosynthesis of spermine and spermidine. It is a class 1B AdoMetDC and belongs to a small family of decarboxylating enzymes that act on amino acids using bound pyruvate as an electron sink. AdoMetDC is synthesised as a proenzyme and must undergo self-maturation by nonhydrolytic serinolysis. It is during this process that the pyruvate group is formed at the carboxy terminus of the alpha chain.	Defined by 5 residues: GLU:A-74 [auth A-62]SER:A-75 [auth A-63]CYS:A-95 [auth A-83]SER:B-67 [auth B-55]HIS:B-80 [auth B-68] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.1.50 (PDB Primary Data) Search M-CSA Motif + EC 4.1.1.50

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.