1KJQ | pdb_00001kjq

Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-ADP

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)
B	d1kjqb1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Glycinamide ribonucleotide transformylase PurT, C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1kjqb2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Glycinamide ribonucleotide transformylase PurT, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1kjqb3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Glycinamide ribonucleotide transformylase PurT, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1kjqa1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Glycinamide ribonucleotide transformylase PurT, C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1kjqa2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Glycinamide ribonucleotide transformylase PurT, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1kjqa3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Glycinamide ribonucleotide transformylase PurT, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Rudiment single hybrid motif	8040374	3001910	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8040377	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8040379	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8040377	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8040379	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rudiment single hybrid motif	8040374	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)
B	LRR_6,LRR_RI_capping	e1kjqB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: LRR_6,LRR_RI_capping	ECOD (develop294)
B	Biotin_carb_C	e1kjqB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
B	RS_preATP-grasp-like	e1kjqB3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RS_preATP-grasp-like	ECOD (develop294)
A	CPSase_L_D2	e1kjqA1	A: beta duplicates or obligate multimers	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: CPSase_L_D2	ECOD (develop294)
A	Biotin_carb_C	e1kjqA2	A: few secondary structure elements	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (develop294)
A	Biotin_carb_N	e1kjqA3	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21244	PurT, C-terminal (PurT_C)	PurT, C-terminal	Formate-dependent phosphoribosylglycinamide formyltransferase (PurT) is involved in de novo purine biosynthesis. PurT belongs to the ATP-grasp superfamily of enzymes and catalyses the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), produ ...	Formate-dependent phosphoribosylglycinamide formyltransferase (PurT) is involved in de novo purine biosynthesis. PurT belongs to the ATP-grasp superfamily of enzymes and catalyses the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) [1,2]. This entry represents the C-terminal domain which has a rudiment single hybrid motif consisting of a sandwich of half-barrel shaped beta-sheets [2].	Domain
A, B	PF22660	Ribonucleotide synthetase preATP-grasp domain (RS_preATP-grasp-like)	Ribonucleotide synthetase preATP-grasp domain	This domain precedes the ATP-grasp domain in a number of ribonucleotide synthetases [1-5].	Domain
A, B	PF02222	ATP-grasp domain (ATP-grasp)	ATP-grasp domain	This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	phosphoribosylglycinamide formyltransferase 2	kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity acetate kinase activity transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity acetate kinase activity transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding phosphoribosylglycinamide formyltransferase activity transferase activity, transferring one-carbon groups hydroxymethyl-, formyl- and related transferase activity acid-ammonia (or amide) ligase activity ligase activity, forming carbon-nitrogen bonds phosphoribosylglycinamide formyltransferase 2 activity ligase activity	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 nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic 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 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011761	ATP-grasp fold	Domain
A, B	IPR054350	PurT/PurK-like, preATP-grasp domain	Domain
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR003135	ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type	Domain
A, B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, B	IPR048740	PurT, C-terminal	Domain
A, B	IPR005862	Formate-dependent phosphoribosylglycinamide formyltransferase	Family

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.