2VD6 | pdb_00002vd6

Human adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-AMP, and its products AMP and fumarate.

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	d2vd6d_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2vd6c_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2vd6b_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2vd6a_	All alpha proteins	L-aspartase-like	L-aspartase-like	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)
D	SCOP2B Superfamily	L-aspartase-like	8085907	3001572	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartase-like	8085907	3001572	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8085907	3001572	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L-aspartase-like	8085907	3001572	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	Rpf1_C	e2vd6D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
D	tRNA-synt_1_2	e2vd6D3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
C	Semialdhyde_dhC	e2vd6C2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Semialdhyde_dhC	ECOD (v294.1)
B	Rpf1_C	e2vd6B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
B	tRNA-synt_1_2	e2vd6B3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
A	Rpf1_C	e2vd6A1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
A	tRNA-synt_1_2	e2vd6A3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
D	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
D	6.10.250.1570	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
C	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
C	6.10.250.1570	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
B	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
B	6.10.250.1570	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
A	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
A	6.10.250.1570	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00206	Lyase (Lyase_1)	Lyase		Domain
A, B, C, D	PF10397	Adenylosuccinate lyase C-terminus (ADSL_C)	Adenylosuccinate lyase C-terminus	This is the C-terminal seven alpha helices of the structure whose full length represents the enzyme adenylosuccinate lyase. This sequence lies C-terminal to the conserved motif necessary for beta-elimination reactions [1], Adenylosuccinate lyase cata ...	This is the C-terminal seven alpha helices of the structure whose full length represents the enzyme adenylosuccinate lyase. This sequence lies C-terminal to the conserved motif necessary for beta-elimination reactions [1], Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide, the eighth step of the de novo pathway, and the formation of adenosine monophosphate (AMP) from adenylosuccinate, the second step in the conversion of inosine monophosphate into AMP [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	ADENYLOSUCCINATE LYASE	N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity amidine-lyase activity lyase activity catalytic activity carbon-nitrogen lyase activity (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity identical protein binding protein binding binding	response to stimulus response to activity response to muscle activity ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process response to stimulus response to activity response to muscle activity ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process AMP biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process nucleotide salvage metabolic compound salvage purine nucleotide salvage AMP salvage purine-containing compound salvage purine ribonucleotide salvage IMP metabolic process IMP biosynthetic process 'de novo' IMP biosynthetic process 'de novo' AMP biosynthetic process GMP metabolic process GMP biosynthetic process aerobic respiration cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus 'de novo' XMP biosynthetic process XMP metabolic process XMP biosynthetic process response to nutrient levels response to chemical response to nutrient response to starvation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000362	Fumarate lyase family	Family
A, B, C, D	IPR022761	Fumarate lyase, N-terminal	Domain
A, B, C, D	IPR008948	L-Aspartase-like	Homologous Superfamily
A, B, C, D	IPR004769	Adenylosuccinate lyase	Family
A, B, C, D	IPR020557	Fumarate lyase, conserved site	Conserved Site
A, B, C, D	IPR019468	Adenylosuccinate lyase C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P30566	adenylosuccinate lyase deficiency autism acute myeloid leukemia cholelithiasis estrogen-receptor negative breast cancer large cell medulloblastoma ovarian cancer Autistic Disorder epilepsy glioblastoma lung cancer psoriasis arthrogryposis breast carcinoma intellectual disability adenylosuccinate lyase deficiency autism acute myeloid leukemia cholelithiasis estrogen-receptor negative breast cancer large cell medulloblastoma ovarian cancer Autistic Disorder epilepsy glioblastoma lung cancer psoriasis arthrogryposis breast carcinoma intellectual disability medulloblastoma uterine corpus leiomyoma

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.