1KY5 | pdb_00001ky5

D244E mutant S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints

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	d1ky5a1	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	d1ky5a2	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	d1ky5b1	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	d1ky5b2	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	d1ky5d1	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	d1ky5d2	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	d1ky5c1	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	d1ky5c2	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)
D	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	FAD_binding_3	e1ky5A1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
A	NAD_binding_1	e1ky5A2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)
B	FAD_binding_3	e1ky5B1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
B	NAD_binding_1	e1ky5B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)
D	FAD_binding_3	e1ky5D1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
D	NAD_binding_1	e1ky5D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)
C	FAD_binding_3	e1ky5C1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
C	NAD_binding_1	e1ky5C2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)

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)
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)
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)

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 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 binding nucleoside phosphate binding purine nucleotide 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 S-adenosylmethionine 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 S-adenosylmethionine cycle S-adenosylmethionine 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 catabolic process oxoacid metabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process nucleobase-containing compound metabolic process non-proteinogenic amino acid metabolic process nucleobase-containing small molecule metabolic process carboxylic acid catabolic process amino acid catabolic process purine ribonucleoside metabolic process carbohydrate derivative catabolic process non-proteinogenic amino acid catabolic process L-amino acid catabolic process carboxylic acid metabolic process modified amino acid metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process S-adenosylhomocysteine metabolic process modified amino acid catabolic process nucleoside metabolic process S-adenosylhomocysteine catabolic process L-amino acid metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process sulfur compound catabolic process alpha-amino acid catabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process purine nucleoside metabolic process purine ribonucleoside catabolic process ribonucleoside metabolic process rhythmic process behavior circadian sleep/wake cycle circadian behavior multicellular organismal process rhythmic behavior circadian rhythm S-methylmethionine cycle S-methylmethionine metabolic process	membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cytosol nucleus membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure 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 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.