1D4F

CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE

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)
A	d1d4fa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1d4fa2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	S-adenosylhomocystein hydrolase	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1d4fb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1d4fb2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	S-adenosylhomocystein hydrolase	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1d4fc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1d4fc2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	S-adenosylhomocystein hydrolase	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1d4fd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1d4fd2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	S-adenosylhomocystein hydrolase	S-adenosylhomocystein hydrolase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8089680	3000044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8089680	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8089680	3000044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8089680	3000044	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)
A	AdoHcyase_NAD	e1d4fA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AdoHcyase_NAD	ECOD (1.6)
A	AdoHcyase	e1d4fA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AdoHcyase	ECOD (1.6)
B	AdoHcyase_NAD	e1d4fB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AdoHcyase_NAD	ECOD (1.6)
B	AdoHcyase	e1d4fB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AdoHcyase	ECOD (1.6)
C	AdoHcyase_NAD	e1d4fC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AdoHcyase_NAD	ECOD (1.6)
C	AdoHcyase	e1d4fC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AdoHcyase	ECOD (1.6)
D	AdoHcyase_NAD	e1d4fD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: AdoHcyase_NAD	ECOD (1.6)
D	AdoHcyase	e1d4fD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: AdoHcyase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1480	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Adenosylhomocysteinase-like	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.1480	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Adenosylhomocysteinase-like	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.1480	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Adenosylhomocysteinase-like	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.1480	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Adenosylhomocysteinase-like	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05221	S-adenosyl-L-homocysteine hydrolase (AdoHcyase)	S-adenosyl-L-homocysteine hydrolase	-	Domain
A, B, C, D	PF00670	S-adenosyl-L-homocysteine hydrolase, NAD binding domain (AdoHcyase_NAD)	S-adenosyl-L-homocysteine hydrolase, NAD binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	S-ADENOSYLHOMOCYSTEINE HYDROLASE	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding trialkylsulfonium hydrolase activity hydrolase activity, acting on ether bonds adenosylselenohomocysteinase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-sulfur bonds binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding trialkylsulfonium hydrolase activity hydrolase activity, acting on ether bonds adenosylselenohomocysteinase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-sulfur bonds adenosylhomocysteinase activity cation binding transition metal ion binding copper ion binding ion binding metal ion binding NAD binding identical protein binding protein binding	S-adenosylmethionine cycle organic substance metabolic process S-adenosylmethionine metabolic process cellular metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process one-carbon metabolic process chronic inflammatory response response to stimulus defense response immune response response to stress S-adenosylmethionine cycle organic substance metabolic process S-adenosylmethionine metabolic process cellular metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process one-carbon metabolic process chronic inflammatory response response to stimulus defense response immune response response to stress immune system process chronic inflammatory response to antigenic stimulus inflammatory response inflammatory response to antigenic stimulus response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus response to nutrient levels response to chemical response to nutrient oxoacid metabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process nucleobase-containing compound metabolic process non-proteinogenic amino acid metabolic process carboxylic acid catabolic process amino acid catabolic process organonitrogen compound catabolic process non-proteinogenic amino acid catabolic process primary metabolic process purine-containing compound catabolic process nucleoside metabolic process S-adenosylhomocysteine catabolic process L-amino acid metabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process sulfur compound catabolic process alpha-amino acid catabolic process nucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process purine ribonucleoside catabolic process ribonucleoside metabolic process cellular modified amino acid catabolic process catabolic process glycosyl compound metabolic process alpha-amino acid metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside metabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process L-amino acid catabolic process carboxylic acid metabolic process glycosyl compound catabolic process S-adenosylhomocysteine metabolic process organic cyclic compound catabolic process cellular modified amino acid metabolic process purine-containing compound metabolic process nucleobase-containing small molecule catabolic process organic substance catabolic process purine nucleoside metabolic process rhythmic process behavior circadian sleep/wake cycle circadian behavior multicellular organismal process rhythmic behavior circadian rhythm	membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytosol nucleus membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytosol nucleus endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000043	Adenosylhomocysteinase-like	Family
A, B, C, D	IPR015878	S-adenosyl-L-homocysteine hydrolase, NAD binding domain	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR020082	S-adenosyl-L-homocysteine hydrolase, conserved site	Conserved Site
A, B, C, D	IPR042172	Adenosylhomocysteinase-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.