1VKZ

Crystal structure of Phosphoribosylamine--glycine ligase (TM1250) from Thermotoga maritima at 2.30 A resolution

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	d1vkza1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Glycinamide ribonucleotide synthetase (GAR-syn), C-domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vkza2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Glycinamide ribonucleotide synthetase (GAR-syn), N-domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vkza3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Glycinamide ribonucleotide synthetase (GAR-syn), domain 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vkzb1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Glycinamide ribonucleotide synthetase (GAR-syn), C-domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vkzb2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Glycinamide ribonucleotide synthetase (GAR-syn), N-domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vkzb3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Glycinamide ribonucleotide synthetase (GAR-syn), domain 2	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	BC ATP-binding domain-like	8029029	4002053	SCOP2 (2022-06-29)
A	SCOP2 Family	BC N-terminal domain-like	8029045	4003858	SCOP2 (2022-06-29)
A	SCOP2 Family	BC C-terminal domain-like	8029043	4002928	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutathione synthetase ATP-binding domain-like	8041408	3000094	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PreATP-grasp domain	8041424	3001680	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Rudiment single hybrid motif	8041422	3001910	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8041408	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8041424	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rudiment single hybrid motif	8041422	3001910	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	ATP-grasp	e1vkzA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
A	GARS_C	e1vkzA2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: GARS_C	ECOD (1.6)
A	GARS_N	e1vkzA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: GARS_N	ECOD (1.6)
B	ATP-grasp	e1vkzB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
B	GARS_C	e1vkzB2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: GARS_C	ECOD (1.6)
B	GARS_N	e1vkzB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: GARS_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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	ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process organonitrogen compound 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 organic substance metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process organonitrogen compound 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 organic substance 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 organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process organic cyclic compound metabolic process IMP biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound 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 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 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.