4M3P | pdb_00004m3p

Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine

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)
D	d4m3pd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Homocysteine S-methyltransferase	Homocysteine S-methyltransferase	Betaine-homocysteine S-methyltransferase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4m3pc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Homocysteine S-methyltransferase	Homocysteine S-methyltransferase	Betaine-homocysteine S-methyltransferase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4m3pb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Homocysteine S-methyltransferase	Homocysteine S-methyltransferase	Betaine-homocysteine S-methyltransferase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4m3pa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Homocysteine S-methyltransferase	Homocysteine S-methyltransferase	Betaine-homocysteine S-methyltransferase	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)
D	SCOP2B Superfamily	Homocysteine S-methyltransferase	8043108	3001844	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homocysteine S-methyltransferase	8043108	3001844	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homocysteine S-methyltransferase	8043108	3001844	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Homocysteine S-methyltransferase	8043108	3001844	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	Rv3651-like_N	e4m3pD1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: Rv3651-like_N	ECOD (v294.1)
C	Hormone_recep	e4m3pC1	A: a/b three-layered sandwiches	X: Outer membrane meander beta-barrels	H: Porins	T: Porin	F: Hormone_recep	ECOD (v294.1)
B	Bact_lectin	e4m3pB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: Bact_lectin	ECOD (v294.1)
A	Rv3651-like_N	e4m3pA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: Rv3651-like_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.330	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Homocysteine-binding-like domain	CATH (4.3.0)
C	3.20.20.330	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Homocysteine-binding-like domain	CATH (4.3.0)
B	3.20.20.330	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Homocysteine-binding-like domain	CATH (4.3.0)
A	3.20.20.330	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Homocysteine-binding-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02574	Homocysteine S-methyltransferase (S-methyl_trans)	Homocysteine S-methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Betaine--homocysteine S-methyltransferase 1	transferase activity, transferring one-carbon groups S-methyltransferase activity betaine-homocysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process L-methionine metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process small molecule biosynthetic process oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process L-methionine metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process protein methylation macromolecule methylation protein alkylation methylation macromolecule modification protein metabolic process macromolecule metabolic process protein modification process 'de novo' L-methionine biosynthetic process catabolic process amino-acid betaine catabolic process modified amino acid metabolic process modified amino acid catabolic process amino-acid betaine metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051524	Betaine-homocysteine S-methyltransferase	Family
A, B, C, D	IPR017226	Betaine-homocysteine S-methyltransferase-like	Family
A, B, C, D	IPR003726	Homocysteine-binding domain	Domain
A, B, C, D	IPR036589	Homocysteine-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q93088	Wilson disease neural tube defect type 2 diabetes mellitus lymphosarcoma non-Hodgkin lymphoma placental abruption Abruptio Placentae reticulum cell sarcoma craniorachischisis tethered spinal cord syndrome iniencephaly maturity-onset diabetes of the young osteosarcoma psoriasis interstitial cystitis Wilson disease neural tube defect type 2 diabetes mellitus lymphosarcoma non-Hodgkin lymphoma placental abruption Abruptio Placentae reticulum cell sarcoma craniorachischisis tethered spinal cord syndrome iniencephaly maturity-onset diabetes of the young osteosarcoma psoriasis interstitial cystitis nephrosclerosis neurenteric cyst ovarian cancer diastematomyelia gastric carcinoma hyperhomocysteinemia

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.