5NX9

Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL) in complex with 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5nx9a_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Homo sapiens neanderthalensis ) [TaxId: 63221 ],	SCOPe (2.08)
D	d5nx9d_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Homo sapiens neanderthalensis ) [TaxId: 63221 ],	SCOPe (2.08)
B	d5nx9b_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Homo sapiens neanderthalensis ) [TaxId: 63221 ],	SCOPe (2.08)
C	d5nx9c_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Homo sapiens neanderthalensis ) [TaxId: 63221 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	L-aspartase-like	8094275	3001572	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L-aspartase-like	8094275	3001572	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8094275	3001572	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartase-like	8094275	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)
A	Adenylsuccinate_lyase_2	e5nx9A2	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Adenylsuccinate_lyase_2	ECOD (1.6)
A	ADSL_C_1	e5nx9A3	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: ADSL_C_1	ECOD (1.6)
A	Lyase_1_C	e5nx9A1	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_1_C	ECOD (1.6)
D	Adenylsuccinate_lyase_2	e5nx9D1	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Adenylsuccinate_lyase_2	ECOD (1.6)
D	ADSL_C_1	e5nx9D2	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: ADSL_C_1	ECOD (1.6)
D	Lyase_1_C	e5nx9D3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_1_C	ECOD (1.6)
B	Adenylsuccinate_lyase_2	e5nx9B1	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Adenylsuccinate_lyase_2	ECOD (1.6)
B	ADSL_C_1	e5nx9B2	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: ADSL_C_1	ECOD (1.6)
B	Lyase_1_C	e5nx9B3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_1_C	ECOD (1.6)
C	Adenylsuccinate_lyase_2	e5nx9C1	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Adenylsuccinate_lyase_2	ECOD (1.6)
C	ADSL_C_1	e5nx9C3	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: ADSL_C_1	ECOD (1.6)
C	Lyase_1_C	e5nx9C2	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_1_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

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 binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic 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 ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic 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 ribonucleoside monophosphate 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 IMP biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process 'de novo' IMP biosynthetic process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process 'de novo' AMP biosynthetic process AMP metabolic process AMP biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR004769	Adenylosuccinate lyase	Family
A, B, C, D	IPR008948	L-Aspartase-like	Homologous Superfamily
A, B, C, D	IPR020557	Fumarate lyase, conserved site	Conserved Site
A, B, C, D	IPR019468	Adenylosuccinate lyase C-terminal	Domain

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.