2OOV

Crystal Structure of Hansenula polymorpha amine oxidase to 1.7 Angstroms

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2oova1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Copper amine oxidase, domain 3	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
A	d2oova2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Copper amine oxidase, domains 1 and 2	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
B	d2oovb1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Copper amine oxidase, domain 3	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
B	d2oovb2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Copper amine oxidase, domains 1 and 2	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
C	d2oovc1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Copper amine oxidase, domain 3	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
C	d2oovc2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Copper amine oxidase, domains 1 and 2	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
D	d2oovd1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Copper amine oxidase, domain 3	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
D	d2oovd2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Copper amine oxidase, domains 1 and 2	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
E	d2oove1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Copper amine oxidase, domain 3	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
E	d2oove2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Copper amine oxidase, domains 1 and 2	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
F	d2oovf1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Copper amine oxidase, domain 3	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)
F	d2oovf2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Copper amine oxidase, domains 1 and 2	(Ogataea angusta ) [TaxId: 870730 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Amine oxidase N-terminal region	8043596	3000455	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Amine oxidase N-terminal region	8043598	3000455	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	amine oxidase catalytic domain	8043593	3001726	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Amine oxidase N-terminal region	8043596	3000455	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Amine oxidase N-terminal region	8043598	3000455	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	amine oxidase catalytic domain	8043593	3001726	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Amine oxidase N-terminal region	8043596	3000455	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Amine oxidase N-terminal region	8043598	3000455	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	amine oxidase catalytic domain	8043593	3001726	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	amine oxidase catalytic domain	8043593	3001726	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Amine oxidase N-terminal region	8043598	3000455	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Amine oxidase N-terminal region	8043596	3000455	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Amine oxidase N-terminal region	8043598	3000455	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Amine oxidase N-terminal region	8043596	3000455	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	amine oxidase catalytic domain	8043593	3001726	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Amine oxidase N-terminal region	8043598	3000455	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Amine oxidase N-terminal region	8043596	3000455	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	amine oxidase catalytic domain	8043593	3001726	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	Cu_amine_oxid	e2oovA1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
A	Cu_amine_oxidN2	e2oovA2	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
A	Cu_amine_oxidN3	e2oovA3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)
B	Cu_amine_oxid	e2oovB1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
B	Cu_amine_oxidN2	e2oovB2	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
B	Cu_amine_oxidN3	e2oovB3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)
C	Cu_amine_oxid	e2oovC1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
C	Cu_amine_oxidN2	e2oovC2	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
C	Cu_amine_oxidN3	e2oovC3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)
D	Cu_amine_oxid	e2oovD1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
D	Cu_amine_oxidN2	e2oovD2	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
D	Cu_amine_oxidN3	e2oovD3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)
E	Cu_amine_oxid	e2oovE1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
E	Cu_amine_oxidN2	e2oovE2	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
E	Cu_amine_oxidN3	e2oovE3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)
F	Cu_amine_oxid	e2oovF1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
F	Cu_amine_oxidN2	e2oovF2	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
F	Cu_amine_oxidN3	e2oovF3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
B	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
B	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
C	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
C	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
D	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
D	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
E	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
E	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
F	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
F	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02728	Copper amine oxidase, N3 domain (Cu_amine_oxidN3)	Copper amine oxidase, N3 domain	This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quino ...	This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).	Domain
A, B	PF02727	Copper amine oxidase, N2 domain (Cu_amine_oxidN2)	Copper amine oxidase, N2 domain	This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quino ...	This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).	Domain
A, B	PF01179	Copper amine oxidase, enzyme domain (Cu_amine_oxid)	Copper amine oxidase, enzyme domain	Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dime ...	Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme.	Domain
C, D, E, F	PF02728	Copper amine oxidase, N3 domain (Cu_amine_oxidN3)	Copper amine oxidase, N3 domain	This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quino ...	This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).	Domain
C, D, E, F	PF02727	Copper amine oxidase, N2 domain (Cu_amine_oxidN2)	Copper amine oxidase, N2 domain	This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quino ...	This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).	Domain
C, D, E, F	PF01179	Copper amine oxidase, enzyme domain (Cu_amine_oxid)	Copper amine oxidase, enzyme domain	Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dime ...	Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Peroxisomal copper amine oxidase	binding quinone binding small molecule binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding	amine metabolic process organonitrogen compound metabolic process organic substance metabolic process metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle
C, D, E, F	Peroxisomal copper amine oxidase	binding quinone binding small molecule binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding	amine metabolic process organonitrogen compound metabolic process organic substance metabolic process metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000269	Copper amine oxidase	Family
A, B	IPR036460	Copper amine oxidase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR015798	Copper amine oxidase, catalytic domain	Domain
A, B	IPR016182	Copper amine oxidase, N-terminal	Homologous Superfamily
A, B	IPR015802	Copper amine oxidase, N3-terminal	Domain
A, B	IPR015800	Copper amine oxidase, N2-terminal	Domain
C, D, E, F	IPR000269	Copper amine oxidase	Family
C, D, E, F	IPR036460	Copper amine oxidase, catalytic domain superfamily	Homologous Superfamily
C, D, E, F	IPR015798	Copper amine oxidase, catalytic domain	Domain
C, D, E, F	IPR016182	Copper amine oxidase, N-terminal	Homologous Superfamily
C, D, E, F	IPR015802	Copper amine oxidase, N3-terminal	Domain
C, D, E, F	IPR015800	Copper amine oxidase, N2-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	SME	Parent Component: MET RESID: AA0581 PSI-MOD : L-methionine (S)-sulfoxide MOD:00721
A, B	TPQ	Parent Component: TYR RESID: AA0581 , AA0147 PSI-MOD : L-methionine (S)-sulfoxide MOD:00721 , oxidation of tyrosine to L-2',4',5'-topaquinone MOD:00156
C, D, E, F	TPQ	Parent Component: TYR RESID: AA0581 , AA0147 , AA0147 PSI-MOD : L-methionine (S)-sulfoxide MOD:00721 , oxidation of tyrosine to L-2',4',5'-topaquinone MOD:00156 , oxidation of tyrosine to L-2',4',5'-topaquinone MOD:00156

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.