2QQD | pdb_00002qqd

N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

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)
H	d2qqdh_	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
G	d2qqdg_	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
F	d2qqdf_	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d2qqdc_	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	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)
H	Me-amine-dh_H	e2qqdH1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (develop294)
G	Me-amine-dh_H	e2qqdG1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (develop294)
F	Me-amine-dh_H	e2qqdF1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (develop294)
C	UBA	e2qqdC1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: UBA	ECOD (develop294)
E	YadA_stalk	e2qqdE01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: YadA_stalk	ECOD (develop294)
B	YadA_stalk	e2qqdB01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: YadA_stalk	ECOD (develop294)
D	YadA_stalk	e2qqdD01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: YadA_stalk	ECOD (develop294)
A	YadA_stalk	e2qqdA01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: YadA_stalk	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
G	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
F	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
C	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
E	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
B	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
D	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, G, H	PF01862	Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) (PvlArgDC)	Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)	-	Family
B, E	PF01862	Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) (PvlArgDC)	Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, G, H	Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) (PvlArgDC)	arginine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	-
B, E	Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) (PvlArgDC)	arginine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	-
A, D	Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) (PvlArgDC)	arginine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, G, H	IPR002724	Pyruvoyl-dependent arginine decarboxylase	Family
C, F, G, H	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
C, F, G, H	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily
B, E	IPR002724	Pyruvoyl-dependent arginine decarboxylase	Family
B, E	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
B, E	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily
A, D	IPR002724	Pyruvoyl-dependent arginine decarboxylase	Family
A, D	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
A, D	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily

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.