4WXY | pdb_00004wxy

PLPS (inactive glutaminase mutant) co-crystallized with glutamine and R5P.

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	d4wxya_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
B [auth C]	d4wxyc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
C [auth E]	d4wxye_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
D [auth G]	d4wxyg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
E [auth I]	d4wxyi_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
F [auth K]	d4wxyk_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
G [auth B]	d4wxyb_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
H [auth D]	d4wxyd_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
I [auth F]	d4wxyf_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
J [auth H]	d4wxyh_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
K [auth J]	d4wxyj_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
L	d4wxyl_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
F [auth K]	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8080556	3001405	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8080556	3001405	SCOP2B (2022-06-29)
I [auth F]	SCOP2 Family	Class I glutamine amidotransferases (GAT)	8080555	4003747	SCOP2 (2022-06-29)
I [auth F]	SCOP2 Superfamily	Class I glutamine amidotransferase-like	8080556	3001405	SCOP2 (2022-06-29)
J [auth H]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8080556	3001405	SCOP2B (2022-06-29)
K [auth J]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8080556	3001405	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8080556	3001405	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	SOR_SNZ	e4wxyA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: SOR_SNZ	ECOD (1.6)
B [auth C]	SOR_SNZ	e4wxyC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: SOR_SNZ	ECOD (1.6)
C [auth E]	SOR_SNZ	e4wxyE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: SOR_SNZ	ECOD (1.6)
D [auth G]	SOR_SNZ	e4wxyG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: SOR_SNZ	ECOD (1.6)
E [auth I]	SOR_SNZ	e4wxyI1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: SOR_SNZ	ECOD (1.6)
F [auth K]	SOR_SNZ	e4wxyK1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: SOR_SNZ	ECOD (1.6)
G [auth B]	GATase	e4wxyB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
H [auth D]	GATase	e4wxyD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
I [auth F]	GATase	e4wxyF1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
J [auth H]	GATase	e4wxyH1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
K [auth J]	GATase	e4wxyJ1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
L	GATase	e4wxyL1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B [auth C]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C [auth E]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D [auth G]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E [auth I]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F [auth K]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G [auth B]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
H [auth D]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
I [auth F]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
J [auth H]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
K [auth J]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
L	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, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	PF01680	SOR/SNZ family (SOR_SNZ)	SOR/SNZ family	Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis [1]. This family was formerly known as UPF0019.	Domain
G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], L	PF00117	Glutamine amidotransferase class-I (GATase)	Glutamine amidotransferase class-I		Domain
G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], L	PF01174	SNO glutamine amidotransferase family (SNO)	SNO glutamine amidotransferase family	This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical ...	This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of Pfam:PF01174 and Pfam:PF01680 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	Pyridoxal biosynthesis lyase PdxS	amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity catalytic activity carbon-nitrogen lyase activity	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic process pyridoxal phosphate metabolic process pyridoxine biosynthetic process pyridoxine metabolic process amino acid metabolic process primary metabolic process	-
G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], L	Glutamine amidotransferase subunit PdxT	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity carbon-nitrogen lyase activity	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic process pyridoxal phosphate metabolic process pyridoxine metabolic process glutamine metabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process L-glutamine catabolic process amino acid metabolic process primary metabolic process organic acid catabolic 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 alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex glutaminase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Family
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	IPR033755	PdxS/SNZ N-terminal domain	Domain
G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], L	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], L	IPR002161	Pyridoxal 5'-phosphate synthase subunit PdxT/SNO	Family
G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], G [auth B], H [auth D], I [auth F], J [auth H], K [auth J], L	IPR021196	PdxT/SNO family, conserved site	Conserved Site

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.