1JBQ | pdb_00001jbq

STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE DEPENDENT HEMEPROTEIN

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d1jbqf_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Cystathionine beta-synthase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1jbqe_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Cystathionine beta-synthase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1jbqd_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Cystathionine beta-synthase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1jbqc_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Cystathionine beta-synthase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1jbqb_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Cystathionine beta-synthase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1jbqa_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Cystathionine beta-synthase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
A	SCOP2 Family	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8021936	4000798	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	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	PALP	e1jbqF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
E	PALP	e1jbqE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
D	PALP	e1jbqD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
C	PALP	e1jbqC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
B	PALP	e1jbqB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
A	PALP	e1jbqA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family

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	CYSTATHIONINE BETA-SYNTHASE	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase (NO-forming) activity nitrite reductase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase (NO-forming) activity nitrite reductase activity catalytic activity cation binding S-adenosyl-L-methionine binding sulfur compound binding carbon monoxide binding cystathionine beta-synthase activity hydro-lyase activity lyase activity carbon-oxygen lyase activity nitric oxide binding oxygen binding identical protein binding protein binding protein homodimerization activity protein dimerization activity tetrapyrrole binding heme binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding metal ion binding modified amino acid binding	cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process response to stimulus signaling regulation of JNK cascade biological regulation regulation of signal transduction regulation of MAPK cascade intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus JNK cascade cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process response to stimulus signaling regulation of JNK cascade biological regulation regulation of signal transduction regulation of MAPK cascade intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus JNK cascade intracellular signaling cassette MAPK cascade regulation of cell communication cellular process signal transduction catabolic process oxoacid metabolic process L-cysteine catabolic process sulfur amino acid metabolic process L-cysteine metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid catabolic process small molecule metabolic process sulfur compound metabolic process amino acid catabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process cysteine metabolic process proteinogenic amino acid metabolic process sulfur compound catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process sulfur amino acid catabolic process cysteine catabolic process metabolic process small molecule catabolic process superoxide metabolic process reactive oxygen species metabolic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cerebellum morphogenesis developmental process multicellular organismal process head development hindbrain morphogenesis animal organ development brain development nervous system development multicellular organism development anatomical structure morphogenesis cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development multi-multicellular organism process maternal process involved in female pregnancy reproductive process multicellular organismal reproductive process female pregnancy multi-organism reproductive process small molecule biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process cysteine biosynthetic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process endochondral ossification replacement ossification endochondral bone morphogenesis skeletal system development ossification skeletal system morphogenesis animal organ morphogenesis bone morphogenesis bone development L-serine catabolic process L-serine metabolic process cysteine biosynthetic process from serine homocysteine catabolic process non-proteinogenic amino acid metabolic process homocysteine metabolic process non-proteinogenic amino acid catabolic process transsulfuration homoserine metabolic process cysteine biosynthetic process via cystathionine blood vessel remodeling tissue remodeling nitric oxide mediated signal transduction regulation of nitric oxide mediated signal transduction connective tissue development tissue development cartilage development involved in endochondral bone morphogenesis cartilage development hydrogen sulfide biosynthetic process hydrogen sulfide metabolic process response to nutrient levels response to folic acid response to nutrient response to oxygen-containing compound response to nitrogen compound response to vitamin regulation of tube diameter system process regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality blood circulation regulation of anatomical structure size DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process macromolecule metabolic process DNA protection	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR046342	CBS domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001216	Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site	Binding Site
A, B, C, D, E A, B, C, D, E, F	IPR046353	Cystathionine beta-synthase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005857	Cystathionine beta-synthase	Family
A, B, C, D, E A, B, C, D, E, F	IPR050214	Cysteine synthase/Cystathionine beta-synthase	Family
A, B, C, D, E A, B, C, D, E, F	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000644	CBS domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P35520	homocystinuria classic homocystinuria hyperhomocysteinemia Malnutrition cardiovascular disease type 2 diabetes mellitus hypertensive disorder melanoma non-Hodgkin lymphoma aphasia thoracic aortic aneurysm intellectual disability maturity-onset diabetes of the young peroxisomal disease apraxia homocystinuria classic homocystinuria hyperhomocysteinemia Malnutrition cardiovascular disease type 2 diabetes mellitus hypertensive disorder melanoma non-Hodgkin lymphoma aphasia thoracic aortic aneurysm intellectual disability maturity-onset diabetes of the young peroxisomal disease apraxia reticulum cell sarcoma cataract dementia lymphosarcoma progressive supranuclear palsy bipolar disorder schizophrenia Ehlers-Danlos syndrome inborn errors of metabolism

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.