2YW2 | pdb_00002yw2

Crystal structure of GAR synthetase from Aquifex aeolicus in complex with ATP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d2yw2b3	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d2yw2b1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d2yw2b2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d2yw2a3	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d2yw2a1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d2yw2a2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Bcl-2,BH4	e2yw2B7	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Bcl-2,BH4	ECOD (develop294)
A	Bcl-2,BH4	e2yw2A7	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Bcl-2,BH4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.90.600.10	Alpha Beta	Alpha-Beta Complex	Glycinamide Ribonucleotide Synthetase	Chain A, domain 4	CATH (4.3.0)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.90.600.10	Alpha Beta	Alpha-Beta Complex	Glycinamide Ribonucleotide Synthetase	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02844	Phosphoribosylglycinamide synthetase, N domain (GARS_N)	Phosphoribosylglycinamide synthetase, N domain	Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphor ...	Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF00289). This domain is structurally related to the PreATP-grasp domain.	Domain
A, B	PF01071	Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain (GARS_A)	Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain	Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phospho ...	Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF02786).	Domain
A, B	PF02843	Phosphoribosylglycinamide synthetase, C domain (GARS_C)	Phosphoribosylglycinamide synthetase, C domain	Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphor ...	Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF02787).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphoribosylamine--glycine ligase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphoribosylamine-glycine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion binding	nucleoside phosphate metabolic process nucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process nucleoside phosphate metabolic process nucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process ribonucleotide metabolic process purine nucleoside monophosphate metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process carbohydrate derivative biosynthetic process nucleoside monophosphate biosynthetic process IMP biosynthetic process 'de novo' IMP biosynthetic process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process nucleobase biosynthetic process purine nucleobase metabolic process purine nucleobase biosynthetic process nucleobase metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000115	Phosphoribosylglycinamide synthetase	Family
A, B	IPR011761	ATP-grasp fold	Domain
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR037123	Phosphoribosylglycinamide synthetase, C-domain superfamily	Homologous Superfamily
A, B	IPR020559	Phosphoribosylglycinamide synthetase, conserved site	Conserved Site
A, B	IPR020562	Phosphoribosylglycinamide synthetase, N-terminal	Domain
A, B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, B	IPR020561	Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain	Domain
A, B	IPR020560	Phosphoribosylglycinamide synthetase, C-domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.