6BYF | pdb_00006byf

Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate

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)
I	d6byfi1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
I	d6byfi2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
H	d6byfh1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
H	d6byfh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
G	d6byfg1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
G	d6byfg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
F	d6byff1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
F	d6byff2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E	d6byfe1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E	d6byfe2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d6byfd1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d6byfd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d6byfc1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d6byfc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d6byfb1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d6byfb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d6byfa1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d6byfa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	SCOP2B (2022-06-29)
A	SCOP2 Family	Dual specificity phosphatase-like	8089655	4000437	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Phosphotyrosine protein) phosphatases II	8089656	3000304	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)
I	V-set	e6byfI1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
H	V-set	e6byfH1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
G	V-set	e6byfG1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
F	V-set	e6byfF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
E	V-set	e6byfE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
D	V-set	e6byfD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
C	V-set	e6byfC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
B	V-set	e6byfB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
A	YcaO	e6byfA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: YcaO	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
H	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
G	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
F	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
E	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
D	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
C	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
B	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)

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, I	PF03162	Tyrosine phosphatase family (Y_phosphatase2)	Tyrosine phosphatase family	This family is closely related to the Pfam:PF00102 and Pfam:PF00782 families.	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, I	Tyrosine-protein phosphatase SIW14	pyrophosphatase activity inositol diphosphate tetrakisphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity diphosphoinositol-polyphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity inositol bisdiphosphate tetrakisphosphate diphosphatase activity inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity inositol diphosphate pentakisphosphate diphosphatase activity inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity phosphoric ester hydrolase activity pyrophosphatase activity inositol diphosphate tetrakisphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity diphosphoinositol-polyphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity inositol bisdiphosphate tetrakisphosphate diphosphatase activity inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity inositol diphosphate pentakisphosphate diphosphatase activity inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity	polyol metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process inositol phosphate metabolic process phosphorus metabolic process diphosphoinositol polyphosphate metabolic process cellular component organization organelle organization actin cytoskeleton organization actin filament organization polyol metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process inositol phosphate metabolic process phosphorus metabolic process diphosphoinositol polyphosphate metabolic process cellular component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR020422	Dual specificity protein phosphatase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR020428	Atypical dual-specificity phosphatase Siw14-like, plant and fungi	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR004861	Atypical dual-specificity phosphatase Siw14-like	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.