4RLG | pdb_00004rlg

The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

External Resource: Annotation

Domain Annotation: SCOP2 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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth C]	SCOP2B Superfamily	PLP-dependent transferases	8097566	3000954	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	PLP-dependent transferases	8097566	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8097566	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8097566	3000954	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)
D [auth C]	Pyridoxal_deC	e4rlgC2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
D [auth C]	Aminotran_5_N	e4rlgC1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C [auth D]	Pyridoxal_deC	e4rlgD2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
C [auth D]	Aminotran_5_N	e4rlgD1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	Pyridoxal_deC	e4rlgB2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
B	Aminotran_5_N	e4rlgB1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
A	Pyridoxal_deC	e4rlgA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
A	Aminotran_5_N	e4rlgA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
D [auth C]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C [auth D]	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
C [auth D]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D], D [auth C]	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth D], D [auth C]	Pyridoxal-dependent decarboxylase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D], D [auth C]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C [auth D], D [auth C]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C [auth D], D [auth C]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C [auth D], D [auth C]	IPR002129	Pyridoxal phosphate-dependent decarboxylase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C [auth D], D [auth C]	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128
A, B, C [auth D], D [auth C]	MSE	Parent Component: MET RESID: AA0119

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.