6OVG | pdb_00006ovg

L-Methionine Depletion with an Engineered Human Enzyme Disrupts Prostate Cancer Metabolism

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d6ovgh_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6ovgg_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6ovgf_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6ovge_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6ovgd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6ovgc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6ovgb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6ovga_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	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)
H	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8059625	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8059625	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)
H	Cys_Met_Meta_PP_C	e6ovgH2	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: Cys_Met_Meta_PP_C	ECOD (1.6)
H	Cys_Met_Meta_PP_N	e6ovgH1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
G	Cys_Met_Meta_PP_C	e6ovgG1	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: Cys_Met_Meta_PP_C	ECOD (1.6)
G	Cys_Met_Meta_PP_N	e6ovgG2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
F	Cys_Met_Meta_PP_C	e6ovgF2	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: Cys_Met_Meta_PP_C	ECOD (1.6)
F	Cys_Met_Meta_PP_N	e6ovgF1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
E	Cys_Met_Meta_PP_C	e6ovgE2	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: Cys_Met_Meta_PP_C	ECOD (1.6)
E	Cys_Met_Meta_PP_N	e6ovgE1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
D	Cys_Met_Meta_PP_C	e6ovgD1	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: Cys_Met_Meta_PP_C	ECOD (1.6)
D	Cys_Met_Meta_PP_N	e6ovgD2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
C	Cys_Met_Meta_PP_C	e6ovgC1	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: Cys_Met_Meta_PP_C	ECOD (1.6)
C	Cys_Met_Meta_PP_N	e6ovgC2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
B	Cys_Met_Meta_PP_C	e6ovgB2	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: Cys_Met_Meta_PP_C	ECOD (1.6)
B	Cys_Met_Meta_PP_N	e6ovgB1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
A	Cys_Met_Meta_PP_C	e6ovgA2	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: Cys_Met_Meta_PP_C	ECOD (1.6)
A	Cys_Met_Meta_PP_N	e6ovgA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)

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	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, C, D, E A, B, C, D, E, F, G, H	Cystathionine gamma-lyase	carbon-sulfur lyase activity lyase activity L-cystine L-cysteine-lyase (deaminating) catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding selenocystathionine gamma-lyase activity cystathionine gamma-lyase activity carbon-sulfur lyase activity lyase activity L-cystine L-cysteine-lyase (deaminating) catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding selenocystathionine gamma-lyase activity cystathionine gamma-lyase activity protein binding calmodulin binding homocysteine desulfhydrase activity identical protein binding L-cysteine desulfhydrase activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling peptidyl-lysine modification primary metabolic process protein-pyridoxal-5-phosphate linkage protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process cysteine metabolic process small molecule metabolic process sulfur compound metabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis 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 lipid metabolic process multicellular organismal process smooth muscle cell differentiation regulation of developmental process cellular developmental process positive regulation of smooth muscle cell differentiation regulation of smooth muscle cell differentiation positive regulation of aortic smooth muscle cell differentiation regulation of cell differentiation regulation of aortic smooth muscle cell differentiation muscle cell differentiation muscle structure development positive regulation of developmental process multicellular organism development aortic smooth muscle cell differentiation vascular associated smooth muscle cell differentiation positive regulation of cell differentiation cell differentiation anatomical structure development system development developmental process positive regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation positive regulation of muscle cell differentiation vasculature development circulatory system development regulation of muscle cell differentiation negative regulation of signaling negative regulation of biological process regulation of programmed cell death negative regulation of cell communication negative regulation of apoptotic signaling pathway negative regulation of cellular process negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway homocysteine metabolic process transsulfuration non-proteinogenic amino acid metabolic process homoserine metabolic process cysteine biosynthetic process via cystathionine protein sulfhydration hydrogen sulfide biosynthetic process hydrogen sulfide metabolic process cellular response to topologically incorrect protein endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein cellular response to stress response to stress response to topologically incorrect protein response to endoplasmic reticulum stress response to peptide response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR054542	Cys/Met metabolism enzyme, pyridoxal-phosphate attachment site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

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: P32929	cystathioninuria melanoma Retinal Neovascularization adrenal cortex carcinoma fetal growth restriction inflammatory bowel disease malignant mesothelioma pancreatic ductal adenocarcinoma tuberculosis adrenoleukodystrophy interstitial lung disease malignant pancreatic neoplasm myelodysplastic syndrome pilocytic astrocytoma gastric carcinoma cystathioninuria melanoma Retinal Neovascularization adrenal cortex carcinoma fetal growth restriction inflammatory bowel disease malignant mesothelioma pancreatic ductal adenocarcinoma tuberculosis adrenoleukodystrophy interstitial lung disease malignant pancreatic neoplasm myelodysplastic syndrome pilocytic astrocytoma gastric carcinoma malignant glioma medulloblastoma oligodendroglioma

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.