Annotations: 1N13

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1n13.2	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
L	d1n13.6	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
J	d1n13.5	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
H	d1n13.4	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
F	d1n13.3	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1n13.1	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
K	d1n13.6	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
I	d1n13.5	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
G	d1n13.4	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
E	d1n13.3	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1n13.2	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1n13.1	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Arginine decarboxylase	Arginine decarboxylase	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K	MIF4G	e1n13K1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
I	MIF4G	e1n13I1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
G	MIF4G	e1n13G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
E	MIF4G	e1n13E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
C	MIF4G	e1n13C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
A	MIF4G	e1n13A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
L	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
J	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
H	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)
B	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
K	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
I	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
G	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
E	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	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
B, D, F, H, J B, D, F, H, J, L	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
B, D, F, H, J B, D, F, H, J, L	Pyruvoyl-dependent arginine decarboxylase alpha chain	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 L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine 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, C, E, G, I A, C, E, G, I, K	Pyruvoyl-dependent arginine decarboxylase beta chain	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 L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine 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
B, D, F, H, J B, D, F, H, J, L	IPR002724	Pyruvoyl-dependent arginine decarboxylase	Family
B, D, F, H, J B, D, F, H, J, L	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR002724	Pyruvoyl-dependent arginine decarboxylase	Family
A, C, E, G, I A, C, E, G, I, K	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, L	PYR	: AA0127 : pyruvic acid (Cys) MOD:00136 , pyruvic acid (Ser) MOD:00807 , pyruvic acid MOD:01154 , pyruvic acid (Tyr) MOD:01661

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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.