5WJA

Crystal structure of H107A peptidylglycine alpha-hydroxylating monooxygenase (PHM) 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)
A	d5wjaa1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	PHM/PNGase F	Peptidylglycine alpha-hydroxylating monooxygenase, PHM	Peptidylglycine alpha-hydroxylating monooxygenase, PHM	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth D]	d5wjad1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	PHM/PNGase F	Peptidylglycine alpha-hydroxylating monooxygenase, PHM	Peptidylglycine alpha-hydroxylating monooxygenase, PHM	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PHM/PNGase F	8041543	3001201	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PHM/PNGase F	8041545	3001201	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	PHM/PNGase F	8041543	3001201	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	PHM/PNGase F	8041545	3001201	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	Cu2_monooxygen	e5wjaA2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Cu2_monooxygen	ECOD (1.6)
A	Cu2_monoox_C	e5wjaA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Cu2_monoox_C	ECOD (1.6)
B [auth D]	Cu2_monooxygen	e5wjaD1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Cu2_monooxygen	ECOD (1.6)
B [auth D]	Cu2_monoox_C	e5wjaD2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Cu2_monoox_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.310	Mainly Beta	Sandwich	Jelly Rolls	Copper type II, ascorbate-dependent monooxygenase, N-terminal domain	CATH (4.3.0)
A	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B [auth D]	2.60.120.310	Mainly Beta	Sandwich	Jelly Rolls	Copper type II, ascorbate-dependent monooxygenase, N-terminal domain	CATH (4.3.0)
B [auth D]	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D]	PF01082	Copper type II ascorbate-dependent monooxygenase, N-terminal domain (Cu2_monooxygen)	Copper type II ascorbate-dependent monooxygenase, N-terminal domain	The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.	Domain
A, B [auth D]	PF03712	Copper type II ascorbate-dependent monooxygenase, C-terminal domain (Cu2_monoox_C)	Copper type II ascorbate-dependent monooxygenase, C-terminal domain	The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D]	Peptidyl-glycine alpha-amidating monooxygenase	amidine-lyase activity catalytic activity, acting on a protein lyase activity peptidylamidoglycolate lyase activity catalytic activity carbon-nitrogen lyase activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding peptidylglycine monooxygenase activity amidine-lyase activity catalytic activity, acting on a protein lyase activity peptidylamidoglycolate lyase activity catalytic activity carbon-nitrogen lyase activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding peptidylglycine monooxygenase activity oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen identical protein binding protein binding calcium ion binding chromatin binding organic acid binding carbohydrate binding vitamin binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding kinase binding enzyme binding protein kinase binding zinc ion binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular metabolic process metabolic process cellular process response to stimulus response to chemical response to xenobiotic stimulus developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular metabolic process metabolic process cellular process toxin metabolic process secondary metabolic process mitotic nuclear division mitotic chromosome condensation organelle fission chromosome organization sister chromatid segregation mitotic cell cycle cellular component organization organelle organization nuclear division mitotic cell cycle process chromosome condensation mitotic sister chromatid segregation nuclear chromosome segregation cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process response to metal ion response to zinc ion limb development appendage development response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus regulation of body fluid levels secretion transport mammary gland development gland development biological regulation establishment of localization body fluid secretion localization lactation regulation of biological quality lipid biosynthetic process amide biosynthetic process fatty acid derivative biosynthetic process primary metabolic process fatty acid primary amide metabolic process fatty acid derivative metabolic process fatty acid primary amide biosynthetic process biosynthetic process amide metabolic process lipid metabolic process peptide metabolic process response to copper ion regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization multi-multicellular organism process maternal process involved in female pregnancy reproductive process multicellular organismal reproductive process female pregnancy multi-organism reproductive process fatty acid metabolic process long-chain fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process cellular lipid metabolic process small molecule metabolic process monocarboxylic acid metabolic process response to corticosteroid response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid response to organic cyclic compound response to pH rhythmic process ovulation cycle ovulation cycle process peptide modification peptide amidation cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process response to estradiol response to oxygen-containing compound	somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network perinuclear region of cytoplasm extracellular region extracellular space transport vesicle membrane transport vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane condensed chromosome cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D]	IPR001258	NHL repeat	Repeat
A, B [auth D]	IPR036939	Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily	Homologous Superfamily
A, B [auth D]	IPR000323	Copper type II, ascorbate-dependent monooxygenase, N-terminal	Domain
A, B [auth D]	IPR008977	PHM/PNGase F domain superfamily	Homologous Superfamily
A, B [auth D]	IPR014783	Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site	Conserved Site
A, B [auth D]	IPR024548	Copper type II ascorbate-dependent monooxygenase, C-terminal	Domain
A, B [auth D]	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A, B [auth D]	IPR020611	Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site	Conserved Site
A, B [auth D]	IPR014784	Copper type II, ascorbate-dependent monooxygenase-like, C-terminal	Homologous Superfamily
A, B [auth D]	IPR000720	Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase	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.