1N9E

Crystal structure of Pichia pastoris Lysyl Oxidase PPLO

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1n9ea1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Lysyl oxidase PplO, domain 3	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
A	d1n9ea2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Lysyl oxidase PplO, domains 1 and 2	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
B	d1n9eb1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Lysyl oxidase PplO, domain 3	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
B	d1n9eb2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Lysyl oxidase PplO, domains 1 and 2	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
D	d1n9ed1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Lysyl oxidase PplO, domain 3	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
D	d1n9ed2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Lysyl oxidase PplO, domains 1 and 2	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
C	d1n9ec1	All beta proteins	Supersandwich	Amine oxidase catalytic domain	Amine oxidase catalytic domain	Lysyl oxidase PplO, domain 3	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)
C	d1n9ec2	Alpha and beta proteins (a+b)	Cystatin-like	Amine oxidase N-terminal region	Amine oxidase N-terminal region	Lysyl oxidase PplO, domains 1 and 2	(Komagataella pastoris ) [TaxId: 4922 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	amine oxidase catalytic domain	8024327	4002771	SCOP2 (2022-06-29)
A	SCOP2 Family	Amine oxidase N-terminal region	8024329	4001015	SCOP2 (2022-06-29)
A	SCOP2 Family	Amine oxidase N-terminal region	8024330	4001015	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	amine oxidase catalytic domain	8036706	3001726	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Amine oxidase N-terminal region	8036708	3000455	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Amine oxidase N-terminal region	8036709	3000455	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Amine oxidase N-terminal region	8036709	3000455	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	amine oxidase catalytic domain	8036706	3001726	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Amine oxidase N-terminal region	8036708	3000455	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	amine oxidase catalytic domain	8036706	3001726	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Amine oxidase N-terminal region	8036709	3000455	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Amine oxidase N-terminal region	8036708	3000455	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Amine oxidase N-terminal region	8036708	3000455	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	amine oxidase catalytic domain	8036706	3001726	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Amine oxidase N-terminal region	8036709	3000455	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	e1n9eA1	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	e1n9eA2	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	DUF1965	e1n9eA3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: DUF1965	ECOD (1.6)
B	Cu_amine_oxid	e1n9eB1	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	e1n9eB2	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	DUF1965	e1n9eB3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: DUF1965	ECOD (1.6)
D	Cu_amine_oxid	e1n9eD1	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	e1n9eD2	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	DUF1965	e1n9eD3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: DUF1965	ECOD (1.6)
C	Cu_amine_oxid	e1n9eC1	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	e1n9eC2	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	DUF1965	e1n9eC3	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: DUF1965	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF09248	Domain of unknown function (DUF1965) (DUF1965)	Domain of unknown function (DUF1965)	Members of this family of fungal domains adopt a structure that consists of an alpha/beta motif. Their exact function has not, as yet, been determined [1].	Domain
A, B, C, D	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, C, D	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, C, D	LYSYL OXIDASE	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor primary methylamine oxidase activity catalytic activity diamine oxidase activity quinone binding	amine metabolic process metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000269	Copper amine oxidase	Family
A, B, C, D	IPR015328	Domain of unknown function DUF1965	Domain
A, B, C, D	IPR036460	Copper amine oxidase, catalytic domain superfamily	Homologous Superfamily
A, B, C, D	IPR015798	Copper amine oxidase, catalytic domain	Domain
A, B, C, D	IPR015800	Copper amine oxidase, N2-terminal	Domain
A, B, C, D	IPR016182	Copper amine oxidase, N-terminal	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	TPQ	Parent Component: TYR RESID: AA0147 PSI-MOD : oxidation of tyrosine to L-2',4',5'-topaquinone MOD:00156

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.