5VK4 | pdb_00005vk4

Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria gonorrhoeae bound to AMPPNP and magnesium

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	d5vk4b1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	PurM N-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
B	d5vk4b2	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
A	d5vk4a1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	PurM N-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
A	d5vk4a2	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae ) [TaxId: 485 ],	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	APG6	e5vk4B1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.1)
A	APG6	e5vk4A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)
A	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02769	AIR synthase related protein, C-terminal domain (AIRS_C)	AIR synthase related protein, C-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site [1].	Domain
A, B	PF00586	AIR synthase related protein, N-terminal domain (AIRS)	AIR synthase related protein, N-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase fo ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphoribosylformylglycinamidine cyclo-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 phosphoribosylformylglycinamidine cyclo-ligase activity catalytic activity cyclo-ligase activity ligase activity, forming carbon-nitrogen bonds ligase activity phosphoribosylamine-glycine 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 nucleobase biosynthetic process purine nucleobase metabolic process purine nucleobase biosynthetic process adenine biosynthetic process nucleobase metabolic process adenine metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036676	PurM-like, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR010918	PurM-like, C-terminal domain	Domain
A, B	IPR016188	PurM-like, N-terminal domain	Domain
A, B	IPR036921	PurM-like, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR004733	Phosphoribosylformylglycinamidine cyclo-ligase	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.