4UP2 | pdb_00004up2

Crystal structure of Escherichia coli tryptophanase purified from alkaline stressed bacterial culture.

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)
D	d4up2d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Beta-eliminating lyases	Tryptophan indol-lyase (tryptophanase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d4up2c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Beta-eliminating lyases	Tryptophan indol-lyase (tryptophanase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d4up2b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Beta-eliminating lyases	Tryptophan indol-lyase (tryptophanase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d4up2a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Beta-eliminating lyases	Tryptophan indol-lyase (tryptophanase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8037097	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8037097	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8037097	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8037097	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	GCD14	e4up2D1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
C	GCD14	e4up2C1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
B	GCD14	e4up2B1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)
A	GCD14	e4up2A1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: GCD14	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01212	Beta-eliminating lyase (Beta_elim_lyase)	Beta-eliminating lyase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	TRYPTOPHANASE	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding lyase activity catalytic activity cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding lyase activity catalytic activity tryptophanase activity carbon-carbon lyase activity identical protein binding protein binding carbon-sulfur lyase activity L-cysteine desulfhydrase activity	indole-containing compound metabolic process metabolic process cellular process indole metabolic process catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-tryptophan metabolic process carboxylic acid catabolic process small molecule metabolic process indole-containing compound metabolic process metabolic process cellular process indole metabolic process catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-tryptophan metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process aromatic amino acid metabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-tryptophan catabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process indole-containing compound catabolic process small molecule catabolic process	cellular anatomical structure membrane cell pole intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001597	Aromatic amino acid beta-eliminating lyase/threonine aldolase	Domain
A, B, C, D	IPR018176	Tryptophanase, conserved site	Conserved Site
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D	IPR011166	Beta-eliminating lyase family	Family
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR013440	Tryptophanase	Family

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.