Annotations: 1N2M

The S53A Proenzyme Structure of Methanococcus jannaschii.

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)
F	d1n2mf_	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	d1n2me_	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	d1n2md_	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	d1n2mc_	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	d1n2mb_	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	d1n2ma_	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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2B (2022-06-29)
D	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)
B	SCOP2B Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2B (2022-06-29)
A	SCOP2 Family	Arginine decarboxylase	8020633	4003740	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pyruvoyl-dependent histidine and arginine decarboxylases	8033013	3001042	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Prot_inhib_II	e1n2mF1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Prot_inhib_II	ECOD (v294.2)
E	Prot_inhib_II	e1n2mE1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Prot_inhib_II	ECOD (v294.2)
D	Prot_inhib_II	e1n2mD1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Prot_inhib_II	ECOD (v294.2)
C	Prot_inhib_II	e1n2mC1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Prot_inhib_II	ECOD (v294.2)
B	Prot_inhib_II	e1n2mB1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Prot_inhib_II	ECOD (v294.2)
A	Prot_inhib_II	e1n2mA1	A: beta barrels	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Prot_inhib_II	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
B	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)
A	3.50.20.10	Alpha Beta	3-Layer(bba) Sandwich	Pyruvoyl-Dependent Histidine Decarboxylase	Chain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01862	Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) (PvlArgDC)	Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)	Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or argini ...	Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organisms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterised proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. Homologues of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Pyruvoyl-dependent arginine decarboxylase	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
A, B, C, D, E A, B, C, D, E, F	IPR002724	Pyruvoyl-dependent arginine decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily

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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.