3D03 | pdb_00003d03

1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes

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)
F	d3d03f_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	GpdQ-like	Glycerophosphodiesterase GpdQ	Aerobacter aerogenes (Klebsiella aerogenes ) [TaxId: 548 ],	SCOPe (2.08)
E	d3d03e_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	GpdQ-like	Glycerophosphodiesterase GpdQ	Aerobacter aerogenes (Klebsiella aerogenes ) [TaxId: 548 ],	SCOPe (2.08)
D	d3d03d_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	GpdQ-like	Glycerophosphodiesterase GpdQ	Aerobacter aerogenes (Klebsiella aerogenes ) [TaxId: 548 ],	SCOPe (2.08)
C	d3d03c_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	GpdQ-like	Glycerophosphodiesterase GpdQ	Aerobacter aerogenes (Klebsiella aerogenes ) [TaxId: 548 ],	SCOPe (2.08)
B	d3d03b_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	GpdQ-like	Glycerophosphodiesterase GpdQ	Aerobacter aerogenes (Klebsiella aerogenes ) [TaxId: 548 ],	SCOPe (2.08)
A	d3d03a_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	GpdQ-like	Glycerophosphodiesterase GpdQ	Aerobacter aerogenes (Klebsiella aerogenes ) [TaxId: 548 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Metallo-dependent phosphatases	8040366	3001067	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-dependent phosphatases	8040366	3001067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-dependent phosphatases	8040366	3001067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent phosphatases	8040366	3001067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8040366	3001067	SCOP2B (2022-06-29)
A	SCOP2 Family	GpdQ-like	8027987	4002581	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent phosphatases	8040366	3001067	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	PhoD_1	e3d03F1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PhoD_1	ECOD (1.6)
E	PhoD_1	e3d03E1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PhoD_1	ECOD (1.6)
D	PhoD_1	e3d03D1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PhoD_1	ECOD (1.6)
C	PhoD_1	e3d03C1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PhoD_1	ECOD (1.6)
B	PhoD_1	e3d03B1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PhoD_1	ECOD (1.6)
A	PhoD_1	e3d03A1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PhoD_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.60.21.40	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
F	3.30.750.180	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	GpdQ, beta-strand dimerisation domain	CATH (4.3.0)
E	3.60.21.40	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
E	3.30.750.180	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	GpdQ, beta-strand dimerisation domain	CATH (4.3.0)
D	3.60.21.40	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
D	3.30.750.180	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	GpdQ, beta-strand dimerisation domain	CATH (4.3.0)
C	3.60.21.40	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
C	3.30.750.180	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	GpdQ, beta-strand dimerisation domain	CATH (4.3.0)
B	3.60.21.40	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
B	3.30.750.180	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	GpdQ, beta-strand dimerisation domain	CATH (4.3.0)
A	3.60.21.40	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
A	3.30.750.180	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	GpdQ, beta-strand dimerisation domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Phosphohydrolase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophosphodiester phosphodiesterase activity hydrolase activity catalytic activity 3',5'-cyclic-nucleotide phosphodiesterase activity 3',5'-cyclic-AMP phosphodiesterase activity cyclic-nucleotide phosphodiesterase activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR026575	Cyclic nucleotide phosphodiesterase GpdQ/CpdA-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR042283	GpdQ, catalytic alpha/beta sandwich domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050884	Cyclic nucleotide phosphodiesterase class-III	Family
A, B, C, D, E A, B, C, D, E, F	IPR042281	GpdQ, beta-strand dimerisation domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029052	Metallo-dependent phosphatase-like	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.