1PYA

REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1pya.1	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Histidine decarboxylase	Histidine decarboxylase	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
C	d1pya.2	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Histidine decarboxylase	Histidine decarboxylase	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
E	d1pya.3	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Histidine decarboxylase	Histidine decarboxylase	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
B	d1pya.1	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Histidine decarboxylase	Histidine decarboxylase	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
D	d1pya.2	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Histidine decarboxylase	Histidine decarboxylase	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
F	d1pya.3	Alpha and beta proteins (a+b)	Pyruvoyl-dependent histidine and arginine decarboxylases	Pyruvoyl-dependent histidine and arginine decarboxylases	Histidine decarboxylase	Histidine decarboxylase	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	4.10.510.10	Few Secondary Structures	Irregular	Pyruvoyl-Dependent Histidine Decarboxylas	Chain A	CATH (4.3.0)
C	4.10.510.10	Few Secondary Structures	Irregular	Pyruvoyl-Dependent Histidine Decarboxylas	Chain A	CATH (4.3.0)
E	4.10.510.10	Few Secondary Structures	Irregular	Pyruvoyl-Dependent Histidine Decarboxylas	Chain A	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	3.50.20.10	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF02329	Histidine carboxylase PI chain (HDC)	Histidine carboxylase PI chain	Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6.	Domain
B, D, F	PF02329	Histidine carboxylase PI chain (HDC)	Histidine carboxylase PI chain	Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)	histidine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	organonitrogen compound metabolic process organic substance metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process metabolic process small molecule metabolic process cellular process histidine metabolic process organic acid metabolic process	-
B, D, F	PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)	histidine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	organonitrogen compound metabolic process organic substance metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process metabolic process small molecule metabolic process cellular process histidine metabolic process organic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR016106	Histidine decarboxylase proenzyme, N-terminal	Homologous Superfamily
A, C, E	IPR003427	Histidine decarboxylase proenzyme	Family
A, C, E	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
A, C, E	IPR016105	Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain	Homologous Superfamily
B, D, F	IPR016106	Histidine decarboxylase proenzyme, N-terminal	Homologous Superfamily
B, D, F	IPR003427	Histidine decarboxylase proenzyme	Family
B, D, F	IPR016104	Pyruvoyl-dependent histidine/arginine decarboxylase	Homologous Superfamily
B, D, F	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	PYR	RESID: AA0127 PSI-MOD : pyruvic acid (Cys) MOD:00136 , pyruvic acid (Ser) MOD:00807 , pyruvic acid MOD:01154 , pyruvic acid (Tyr) MOD:01661

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

Chains	Enzyme Name	Description	Catalytic Residues
A, E, F	histidine decarboxylase M-CSA #49	Histidine decarboxylasses from Lactobacillus 30a is the best-studied of a class of enzyme which utilise the covalently bound cofactor, pyruvate. Models of the active site with and without the bound substrate analogue, histidine methyl ester (HisOMe), or the product, histamine, have been produced. Comparison of native and ligand-bound structures reveals no widespread differences in conformation but does reveal motion of a few key residues. The native enzyme is an (alpha-beta)₆ \"hexamer\". Two trimers bind bottom-to-bottom across a crystallographic dyad, forming a dumbell-shaped hexamer with cavities at either end.	Defined by 7 residues: TYR:A-62ASP:A-63GLU:A-66SER:E-81UNK:F-1 [auth F-82]PHE:F-114 [auth F-195]GLU:F-116 [auth F-197] \| Explore in 3D: M-CSA Motif Definition Some residues are non-polymeric components. Structure Motif searching is not available. EC: 4.1.1.22 (PDB Primary Data)

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.