4BKM | pdb_00004bkm

Crystal structure of the murine AUM (phosphoglycolate phosphatase) capping domain as a fusion protein with the catalytic core domain of murine chronophin (pyridoxal phosphate phosphatase)

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)
D	d4bkmd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4bkmc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4bkmb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d4bkma_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ], HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	NagD-like	8058825	4001039	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HAD-like	8058826	3001890	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)
D	HAD_2	e4bkmD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
D	UNK_F_TYPE	e4bkmD2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UNK_F_TYPE	ECOD (1.6)
C	HAD_2	e4bkmC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
C	UNK_F_TYPE	e4bkmC2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UNK_F_TYPE	ECOD (1.6)
B	HAD_2	e4bkmB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
B	UNK_F_TYPE	e4bkmB2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UNK_F_TYPE	ECOD (1.6)
A	HAD_2	e4bkmA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
A	UNK_F_TYPE	e4bkmA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
C	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13242	HAD-hyrolase-like (Hydrolase_like)	HAD-hyrolase-like		Domain
A, B, C, D	PF13344	Haloacid dehalogenase-like hydrolase (Hydrolase_6)	Haloacid dehalogenase-like hydrolase	This family is part of the HAD superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE	phosphoric ester hydrolase activity phosphoprotein phosphatase activity protein serine/threonine phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding binding heat shock protein binding cation binding magnesium ion binding ion binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity protein serine/threonine phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding binding heat shock protein binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity pyridoxal phosphatase activity sn-glycerol 3-phosphatase activity pyrophosphatase activity nucleoside diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ADP phosphatase activity hydrolase activity, acting on acid anhydrides phosphoglycolate phosphatase activity sn-glycerol 1-phosphatase activity protein tyrosine phosphatase activity	actin cytoskeleton organization actin rod assembly actin filament organization cellular component biogenesis cellular component organization organelle organization cellular component assembly actin filament bundle organization actin filament bundle assembly actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization actin cytoskeleton organization actin rod assembly actin filament organization cellular component biogenesis cellular component organization organelle organization cellular component assembly actin filament bundle organization actin filament bundle assembly actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size positive regulation of biological process protein-containing complex disassembly positive regulation of actin filament depolymerization regulation of protein-containing complex disassembly actin filament depolymerization regulation of actin filament depolymerization regulation of biological quality positive regulation of protein-containing complex disassembly positive regulation of cellular process cellular component disassembly actin polymerization or depolymerization regulation of biological process regulation of actin filament organization protein-containing complex organization regulation of protein depolymerization positive regulation of protein depolymerization positive regulation of cytoskeleton organization biological regulation regulation of actin polymerization or depolymerization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization protein depolymerization regulation of anatomical structure size vitamin B6 catabolic process pyridoxal phosphate catabolic process catabolic process organophosphate catabolic process aldehyde metabolic process vitamin catabolic process vitamin metabolic process water-soluble vitamin catabolic process organophosphate metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic process aldehyde catabolic process small molecule catabolic process pyridoxal phosphate metabolic process pyridine-containing compound catabolic process protein dephosphorylation dephosphorylation primary metabolic process macromolecule modification protein metabolic process macromolecule metabolic process protein modification process regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division cell cycle regulation of cell cycle cell cycle process mitotic nuclear division organelle fission regulation of mitotic nuclear division mitotic cell cycle regulation of mitotic cell cycle nuclear division mitotic cell cycle process regulation of nuclear division cellular response to nitrogen compound cellular response to stimulus cellular response to ATP response to stimulus response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to ATP response to purine-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical regulation of modification of synaptic structure regulation of synapse organization cell junction organization regulation of synapse structure or activity regulation of modification of postsynaptic structure synapse organization modification of synaptic structure modification of postsynaptic structure carbohydrate metabolic process polyol metabolic process small molecule biosynthetic process glycerol biosynthetic process carbohydrate biosynthetic process alditol biosynthetic process alcohol metabolic process glycerol metabolic process biosynthetic process polyol biosynthetic process alcohol biosynthetic process monosaccharide metabolic process negative regulation of small molecule metabolic process negative regulation of biological process gluconeogenesis regulation of primary metabolic process negative regulation of gluconeogenesis regulation of small molecule metabolic process negative regulation of cellular process regulation of carbohydrate metabolic process regulation of glucose metabolic process negative regulation of carbohydrate metabolic process regulation of biosynthetic process negative regulation of metabolic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process negative regulation of biosynthetic process regulation of gluconeogenesis regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process phospholipid metabolic process glycerophospholipid metabolic process glycerolipid metabolic process lipid metabolic process	midbody cellular anatomical structure cell-cell junction anchoring junction cell junction ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane midbody cellular anatomical structure cell-cell junction anchoring junction cell junction ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol cell division site cleavage furrow synapse glutamatergic synapse lamellipodium membrane lamellipodium postsynapse contractile ring

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006357	HAD-superfamily hydrolase, subfamily IIA	Family
A, B, C, D	IPR006349	2-phosphoglycolate phosphatase, eukaryotic	Family
A, B, C, D	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D	IPR006357	HAD-superfamily hydrolase, subfamily IIA	Family
A, B, C, D	IPR006349	2-phosphoglycolate phosphatase, eukaryotic	Family
A, B, C, D	IPR036412	HAD-like 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.