8S5K | pdb_00008s5k

Full-length human cystathionine beta-synthase, basal state, single particle reconstruction

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)
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	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8034316	3001427	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H	PF00571	CBS domain (CBS)	CBS domain	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands ...	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet [5]. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet [4]. CBS domain pairs from AMPK bind AMP or ATP [5]. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP [5].	Domain

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G, H	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.