Summary: Copper amine oxidase, enzyme domain

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Wikipedia: Amine oxidase (copper-containing)
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Amine oxidase (copper-containing) Edit Wikipedia article

amine oxidase

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PDB structures

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Copper amine oxidase, enzyme domain

Crystal structure of a copper-containing benzylamine oxidase from Hansenula polymorpha.^[1]

Identifiers

Symbol

Cu_amine_oxid

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Copper amine oxidase N-terminal domain

crystal structure of e. coli amine oxidase anaerobically reduced with beta-phenylethylamine

Identifiers

Symbol

Cu_amine_oxidN1

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Copper amine oxidase, N2 domain

crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2a resolution

Identifiers

Symbol

Cu_amine_oxidN2

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Copper amine oxidase, N3 domain

crystal structure of hansenula polymorpha amine oxidase in complex with xe to 1.6 angstroms

Identifiers

Symbol

Cu_amine_oxidN3

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Amine oxidases (AO) are enzymes that catalyze the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (EC 1.4.3.4) and copper-containing (EC 1.4.3.6). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor:^[2]

RCH₂NH₂ + H₂O + O₂ $\rightleftharpoons$ RCHO + NH₃ + H₂O₂

The 3 substrates of this enzyme are primary amines (RCH2NH2), H₂O, and O₂, whereas its 3 products are RCHO, NH₃, and H₂O₂.

Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen.^[3]^[4]

This enzyme belongs to oxidoreductases, specifically those acting on the CH-NH2 group of donors with oxygen as acceptor. The systematic name of this enzyme class is amine:oxygen oxidoreductase (deaminating) (copper-containing). This enzyme participates in 8 metabolic pathways: urea cycle and metabolism of amino groups, glycine, serine and threonine metabolism, histidine metabolism, tyrosine metabolism, phenylalanine metabolism, tryptophan metabolism, beta-alanine metabolism, and alkaloid biosynthesis ii. It has 2 cofactors: copper, and PQQ.

[edit] Structure

The copper amine oxidase 3-dimensional structure was determined through X-ray crystallography.^[1] The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access.

The N2 and N3 N-terminal domains share a common structural fold, its core consisting of alpha-beta(4), where the helix is packed against the coiled anti-parallel beta-sheets. An additional domain is found at the N-terminal of some copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix.^[5]^[6]

[edit] Function

In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling^[7] as well as functioning as a vascular adhesion protein (VAP-1) in some mammalian tissues.^[1]

[edit] Human proteins containing this domain

ABP1; AOC2; AOC3;

[edit] See also

Copper in health

[edit] References

^ ^a ^b ^c PDB 3LOY; Chang CM, Klema VJ, Johnson BJ, Mure M, Klinman JP, Wilmot CM (March 2010). "Kinetic and structural analysis of substrate specificity in two copper amine oxidases from Hansenula polymorpha". Biochemistry 49 (11): 2540–50. doi:10.1021/bi901933d. PMID 20155950.
^ Convery MA, Phillips SE, McPherson MJ, Yadav KD, Knowles PF, Parsons MR, Wilmot CM, Blakeley V, Corner AS (1995). "Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution". Structure 3 (11): 1171–1184. PMID 8591028.
^ Murray JM, Convery MA, Phillips SE, McPherson MJ, Knowles PF, Parsons MR, Wilmot CM, Blakeley V, Corner AS, Alton G, Palcic MM (1997). "Catalytic mechanism of the quinoenzyme amine oxidase from Escherichia coli: exploring the reductive half-reaction". Biochemistry 36 (7): 1608–1620. doi:10.1021/bi962205j. PMID 9048544.
^ Tanizawa K, Guss JM, Freeman HC, Yamaguchi H, Wilce MC, Dooley DM, Matsunami H, Mcintire WS, Ruggiero CE (1997). "Crystal structures of the copper-containing amine oxidase from Arthrobacter globiformis in the holo and apo forms: implications for the biogenesis of topaquinone". Biochemistry 36 (51): 16116–16133. doi:10.1021/bi971797i. PMID 9405045.
^ Parsons MR, Convery MA, Wilmot CM, Yadav KD, Blakeley V, Corner AS, Phillips SE, McPherson MJ, Knowles PF (November 1995). "Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution". Structure 3 (11): 1171–84. PMID 8591028.
^ Wilmot CM, Hajdu J, McPherson MJ, Knowles PF, Phillips SE (November 1999). "Visualization of dioxygen bound to copper during enzyme catalysis". Science 286 (5445): 1724–8. doi:10.1126/science.286.5445.1724. PMID 10576737.
^ Guss JM, Freeman HC, Kumar V, Wilce MC, Dooley DM, Harvey I, Mcguirl MA, Zubak VM (1996). "Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2 A resolution". Structure 4 (8): 943–955. PMID 8805580.

[edit] Further reading

Ameyama M, Hayashi M, Matsushita K, Shinagawa E, Adachi O (1984). "Microbial-production of pyrroloquinoline quinone". Agric. Biol. Chem. 48: 561–565.
Augustinsson KB, Olsson B (1959). "Esterases in the milk and blood plasma of swine. I. Substrate specificity and electrophoresis studies". Biochem. J. 71 (3): 477–84. PMC 1196820. PMID 13638253. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1196820/.
Boyer, P.D., Lardy, H. and Myrback, K. (Eds.), The Enzymes, 2nd ed., vol. 8, Academic Press, New York, 1963, p. 337-351.
Buffoni F, Blaschko H (1964). "Benzylamine oxidase and histaminase: purification and crystallization of an enzyme from pig plasma". Proc. R. Soc. Lond. B. Biol. Sci. 161: 153–67. doi:10.1098/rspb.1964.0086. PMID 14224405.
Haywood GW, Large PJ (1981). "Microbial oxidation of amines. Distribution, purification and properties of two primary-amine oxidases from the yeast Candida boidinii grown on amines as sole nitrogen source". Biochem. J. 199 (1): 187–201. PMC 1163349. PMID 7337701. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1163349/.
McEwen CM Jr (1965). "Human plasma monoamine oxidase. 1. Purification and identification". J. Biol. Chem. 240 (5): 2003–10. PMID 5888801.
Mondovi B, Costa MT, Agro AF, Rotilio G (1967). "Pyridoxal phosphate as a prosthetic group of pig kidney diamine oxidase". Arch. Biochem. Biophys. 119 (1): 373–81. doi:10.1016/0003-9861(67)90468-7. PMID 4964016.
Yamada H, Adachi O and Ogata K (1965). "Amine oxidases of microorganisms. Part II. Purification and crystallisation of amine oxidase of Aspergillus niger". Agric. Biol. Chem. 29: 649–654.
Yamada H, Adachi O and Ogata K (1965). "Amine oxidases of microorganisms. Part III. Properties of amine oxidase of Aspergillus niger". Agric. Biol. Chem. 29: 864–869.
Yamada H, Adachi O and Ogata K (1965). "Amine oxidases of microorganisms. Part IV. Further properties of amine oxidase of Aspergillus niger". Agric. Biol. Chem. 29: 912–917.
Boyer, P.D., Lardy, H. and Myrback, K. (Eds.), The Enzymes, 2nd ed., vol. 8, Academic Press, New York, 1963, p. 313-335.

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Copper amine oxidase, enzyme domain Provide feedback

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.

Literature references

Parsons MR, Convery MA, Wilmot CM, Yadav KD, Blakeley V, Corner AS, Phillips SE, McPherson MJ, Knowles PF; , Structure 1995;3:1171-1184.: Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution. PUBMED:8591028 EPMC:8591028

External database links

HOMSTRAD:	Cu_amine_oxid
PANDIT:	PF01179
PROSITE:	PDOC00895
Pseudofam:	PF01179
SCOP:	1oac
SYSTERS:	Cu_amine_oxid

This tab holds annotation information from the InterPro database.

InterPro entry IPR015798

Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (EC) and copper-containing (EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor [PUBMED:8591028]: RCH₂NH₂ + H₂O + O₂ = RCHO + NH₃ + H₂O₂

Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [PUBMED:9048544, PUBMED:9405045]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling [PUBMED:8805580].

The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [PUBMED:8591028, PUBMED:10576737].

This entry represents the C-terminal catalytic domain of copper amine oxidases, and has a super-sandwich fold consisting of 18 beta-strands in 2 sheets [PUBMED:8591028]. A domain with a similar structural fold can be found as the third domain in lysyl oxidase PplO [PUBMED:14690425].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	primary amine oxidase activity (GO:0008131)
	copper ion binding (GO:0005507)
	quinone binding (GO:0048038)
Biological process	oxidation-reduction process (GO:0055114)
Biological process	amine metabolic process (GO:0009308)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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meta: alignment generated by searching the metagenomics sequence database using the family HMM

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	Seed (75)	Full (1272)	Representative proteomes				NCBI (1240)	Meta (205)
	Seed (75)	Full (1272)	RP15 (162)	RP35 (358)	RP55 (544)	RP75 (699)	NCBI (1240)	Meta (205)
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Format an alignment

	Seed (75)	Full (1272)	Representative proteomes				NCBI (1240)	Meta (205)
	Seed (75)	Full (1272)	RP15 (162)	RP35 (358)	RP55 (544)	RP75 (699)	NCBI (1240)	Meta (205)
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	Seed (75)	Full (1272)	Representative proteomes				NCBI (1240)	Meta (205)
	Seed (75)	Full (1272)	RP15 (162)	RP35 (358)	RP55 (544)	RP75 (699)	NCBI (1240)	Meta (205)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Author:

Bateman A, Finn RD

Number in seed:

75

Number in full:

1272

Average length of the domain:

371.60 aa

Average identity of full alignment:

33 %

Average coverage of the sequence by the domain:

57.94 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	19.7	19.7
Trusted cut-off	20.1	21.4
Noise cut-off	19.5	18.3

Model length:

413

Family (HMM) version:

15

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Species distribution

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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Interactions

There are 5 interactions for this family. More...

Cu_amine_oxid DUF1965 Cu_amine_oxidN2 Cu_amine_oxidN1 Cu_amine_oxidN3

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Cu_amine_oxid domain has been found. There are 187 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Cu_amine_oxid (PF01179)

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Summary: Copper amine oxidase, enzyme domain

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Amine oxidase (copper-containing) Edit Wikipedia article

Contents

[edit] Structure

[edit] Function

[edit] Human proteins containing this domain

[edit] See also

[edit] References

[edit] Further reading

Copper amine oxidase, enzyme domain Provide feedback

Literature references

External database links

InterPro entry IPR015798

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures