4MGH

Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis

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	d4mgha2	All alpha proteins	RuvA C-terminal domain-like	FGAM synthase PurL, linker domain	FGAM synthase PurL, linker domain	FGAM synthase PurL, linker domain	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4mgha7	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	FGAM synthase PurL, amidotransferase domain	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4mgha3	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	PurM N-terminal domain-like	PurM N-terminal domain-like	FGAM synthase PurL, PurM-like module, N1 and N2 domains	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4mgha6	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	PurM C-terminal domain-like	FGAM synthase PurL, PurM-like module, C1 and C2 domains, C-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4mgha4	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	PurM C-terminal domain-like	FGAM synthase PurL, PurM-like module, C1 and C2 domains, N-terminal domain	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4mgha1	Alpha and beta proteins (a+b)	PurS-like	PurS-like	FGAM synthase PurL, PurS-like domain	FGAM synthase PurL, PurS-like domain	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4mgha8	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FGAM synthase PurL, linker domain	8039952	3001116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PurS-like	8039955	3000512	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PurM N-terminal domain-like	8039957	3001759	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PurM C-terminal domain-like	8039959	3000696	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PurM C-terminal domain-like	8039960	3000696	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8039953	3001405	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PurM N-terminal domain-like	8039956	3001759	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	PRK05297_2nd	e4mghA1	A: alpha arrays	X: RuvA-C	H: FGAM synthase PurL, linker domain (From Topology)	T: FGAM synthase PurL, linker domain	F: PRK05297_2nd	ECOD (1.6)
A	PRK05297_1st	e4mghA2	A: a+b two layers	X: Alpha-beta plaits	H: PurS-like (From Topology)	T: PurS-like	F: PRK05297_1st	ECOD (1.6)
A	AIRS_C	e4mghA3	A: a+b two layers	X: Alpha-beta plaits	H: PurM C-terminal domain-like (From Topology)	T: PurM C-terminal domain-like	F: AIRS_C	ECOD (1.6)
A	AIRS	e4mghA6	A: a+b three layers	X: Bacillus chorismate mutase-like	H: PurM N-terminal domain-like (From Topology)	T: PurM N-terminal domain-like	F: AIRS	ECOD (1.6)
A	AIRS_1	e4mghA5	A: a+b three layers	X: Bacillus chorismate mutase-like	H: PurM N-terminal domain-like (From Topology)	T: PurM N-terminal domain-like	F: AIRS_1	ECOD (1.6)
A	GATase_5	e4mghA7	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.750	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18076	Formylglycinamide ribonucleotide amidotransferase N-terminal (FGAR-AT_N)	Formylglycinamide ribonucleotide amidotransferase N-terminal	This is the N-terminal domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme cataly ...	This is the N-terminal domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide and glutamine to formylglycinamidine ribonucleotide, ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway [3].	Domain
A	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	PF13507	CobB/CobQ-like glutamine amidotransferase domain (GATase_5)	CobB/CobQ-like glutamine amidotransferase domain	This family captures members that are not found in Pfam:PF00310, Pfam:PF07685 and Pfam:PF13230.	Domain
A	PF22689	FGAR-AT PurM_N-like domain (FGAR-AT_PurM_N-like)	FGAR-AT PurM_N-like domain	This entry represents the PurM_N-like domain of formylglycinamide ribonucleotide amidotransferase (FGAR-AT) and related proteins. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) to formylglycinamidine ribonuc ...	This entry represents the PurM_N-like domain of formylglycinamide ribonucleotide amidotransferase (FGAR-AT) and related proteins. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) to formylglycinamidine ribonucleotide (FGAM) in the fourth step of the purine biosynthetic pathway. This domain consists of an antiparallel beta-sheet with two helices packed on one side [1-5].	Domain
A	PF18072	Formylglycinamide ribonucleotide amidotransferase linker domain (FGAR-AT_linker)	Formylglycinamide ribonucleotide amidotransferase linker domain	This is the linker domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes ...	This is the linker domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. The structure analysis of Salmonella typhimurium FGAR-AT reveals that this linker domain is made up of a long hydrophilic belt with an extended conformation [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phosphoribosylformylglycinamidine synthase	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 carbon-nitrogen ligase activity, with glutamine as amido-N-donor phosphoribosylformylglycinamidine synthase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion binding	nucleoside phosphate metabolic process cellular 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 metabolic process cellular 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 ribonucleoside monophosphate 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 glutamine metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A	IPR010073	Phosphoribosylformylglycinamidine synthase PurL	Family
A	IPR041609	Phosphoribosylformylglycinamidine synthase, linker domain	Domain
A	IPR036676	PurM-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR036604	Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily	Homologous Superfamily
A	IPR040707	Phosphoribosylformylglycinamidine synthase, N-terminal	Domain
A	IPR010918	PurM-like, C-terminal domain	Domain
A	IPR036921	PurM-like, N-terminal domain superfamily	Homologous Superfamily

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.