1N13 | pdb_00001n13

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
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)
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)
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: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
D	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 carboxylic acid metabolic process L-amino acid catabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process arginine metabolic process L-arginine catabolic process alpha-amino acid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process L-amino acid catabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process arginine 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, 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 carboxylic acid metabolic process L-amino acid catabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process arginine metabolic process L-arginine catabolic process alpha-amino acid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process L-amino acid catabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process arginine 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
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	RESID: AA0127 PSI-MOD : pyruvic acid (Cys) MOD:00136 , pyruvic acid (Ser) MOD:00807 , pyruvic acid MOD:01154 , pyruvic acid (Tyr) MOD:01661

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.