1IBJ | pdb_00001ibj

Crystal structure of cystathionine beta-lyase from Arabidopsis thaliana

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)
B [auth C]	d1ibjc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Cystathionine beta-lyase, CBL	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d1ibja_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Cystathionine beta-lyase, CBL	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	PLP-dependent transferases	8033856	3000954	SCOP2B (2022-06-29)
A	SCOP2 Family	Cystathionine synthase-like	8021476	4000672	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8033856	3000954	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)
B [auth C]		e1ibjC2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)
A	Rubrerythrin	e1ibjA1	A: alpha bundles	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: Rubrerythrin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B [auth C]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	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)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	PF01053	Cys/Met metabolism PLP-dependent enzyme (Cys_Met_Meta_PP)	Cys/Met metabolism PLP-dependent enzyme	This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomose ...	This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	CYSTATHIONINE BETA-LYASE	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding carbon-sulfur lyase activity lyase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding carbon-sulfur lyase activity lyase activity catalytic activity molecular adaptor activity cysteine-S-conjugate beta-lyase activity	homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process L-cysteine metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process transsulfuration alpha-amino acid metabolic process L-amino acid metabolic process cysteine metabolic process proteinogenic amino acid metabolic process non-proteinogenic amino acid metabolic process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process L-cysteine metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process transsulfuration alpha-amino acid metabolic process L-amino acid metabolic process cysteine metabolic process proteinogenic amino acid metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process aspartate family amino acid biosynthetic process organic acid biosynthetic process L-homoserine metabolic process carboxylic acid biosynthetic process L-methionine biosynthetic process from L-homoserine via cystathionine L-methionine biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process methionine metabolic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
A, B [auth C]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B [auth C]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B [auth C]	IPR054542	Cys/Met metabolism enzyme, pyridoxal-phosphate attachment site	Conserved Site
A, B [auth C]	IPR006238	Cystathionine beta-lyase, eukaryotic	Family
A, B [auth C]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

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.