1T70

Crystal structure of a novel phosphatase from Deinococcus radiodurans

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	d1t70a_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
B	d1t70b_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
C	d1t70c_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
D	d1t70d_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
E	d1t70e_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
G	d1t70g_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
H	d1t70h_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
F	d1t70f_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DR1281-like	Putative phosphatase DR1281	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DR1281-like	8030030	4003864	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Metallo-dependent phosphatases	8042409	3001067	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	YmdB	e1t70A1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
B	YmdB	e1t70B1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
C	YmdB	e1t70C1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
D	YmdB	e1t70D1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
E	YmdB	e1t70E1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
G	YmdB	e1t70G1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
H	YmdB	e1t70H1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)
F	YmdB	e1t70F1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: YmdB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
B	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
C	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
D	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
E	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
G	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
H	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
F	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	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, G, H	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, G, H	Phosphatase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity cyclic-nucleotide phosphodiesterase activity catalytic activity 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity phosphoenolpyruvate phosphatase activity phosphatase activity cation binding ion binding binding metal ion binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity cyclic-nucleotide phosphodiesterase activity catalytic activity 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity phosphoenolpyruvate phosphatase activity phosphatase activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005235	Metallophosphoesterase, YmdB-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.