2ZL8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF COPPER AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS: SUBSTRATE SCHIFF-BASE INTERMEDIATE FORMED WITH ETHYLAMINE

Authors :   T. Murakawa, T. Okajima

Date :   03 Apr 08 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

Chains :   Asym./Biol. Unit : A,B

Keywords :   Copper, Amine Oxidase, Topaquinone, Tpq, Reaction Intermediate, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Taki, T. Murakawa, T. Nakamoto, M. Uchida, H. Hayashi, K. Tanizawa, Y. Yamamoto, T. Okajima
Further Insight Into The Mechanism Of Stereoselective Proton Abstraction By Bacterial Copper Amine Oxidase
Biochemistry V. 47 7726 2008
PubMed-ID: 18627131 | Reference-DOI: 10.1021/BI800623F
(for further references see the PDB file header)

Molecule 1 - PHENYLETHYLAMINE OXIDASE
	Chains	:	A, B
	EC Number	:	1.4.3.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEPO-02
	Expression System Strain	:	CD03
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ARTHROBACTER GLOBIFORMIS
	Organism Taxid	:	1665
	Synonym	:	AMINE OXIDASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION
2	ESB	2	Mod. Amino Acid	3-[(3E)-3-(ETHYLIMINO)-4-HYDROXY-6-OXOCYCLOHEXA-1,4-DIEN-1-YL]-L-ALANINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:284 , TYR A:296 , THR A:378 , ILE A:379 , GLY A:380 , ASN A:381 , ASP A:383 , TYR A:384	BINDING SITE FOR RESIDUE ESB A 382
2	AC2	SOFTWARE	LEU B:137 , TYR B:284 , TYR B:296 , THR B:378 , ILE B:379 , GLY B:380 , ASN B:381 , ASP B:383 , TYR B:384 , PHE B:407 , HIS B:433	BINDING SITE FOR RESIDUE ESB B 382
3	AC3	SOFTWARE	HIS A:431 , HIS A:433 , HIS A:592	BINDING SITE FOR RESIDUE CU A 1001
4	AC4	SOFTWARE	HIS B:431 , HIS B:433 , HIS B:592	BINDING SITE FOR RESIDUE CU B 1001

Asymmetric/Biological Unit

No.	Residues
1	A:317	-	A:343
2	B:317	-	B:343

Asymmetric/Biological Unit

No.	Residues
1	Trp A:599	-	Pro A:600
2	Trp B:599	-	Pro B:600

(no "SAP(SNP)/Variant" information available for 2ZL8)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_AMINE_OXID_1	PS01164	Copper amine oxidase topaquinone signature.	PAOX_ARTGO	371-384	2	A:371-384 B:371-384
2	COPPER_AMINE_OXID_2	PS01165	Copper amine oxidase copper-binding site signature.	PAOX_ARTGO	587-600	2	A:587-600 B:587-600

(no "Exon" information available for 2ZL8)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:620
 aligned with PAOX_ARTGO | P46881 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:620
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628
           PAOX_ARTGO     9 ASPFRLASAGEISEVQGILRTAGLLGPEKRIAYLGVLDPARGAGSEAEDRRFRVFIHDVSGARPQEVTVSVTNGTVISAVELDTAATGELPVLEEEFEVVEQLLATDERWLKALAARNLDVSKVRVAPLSAGVFEYAEERGRRILRGLAFVQDFPEDSAWAHPVDGLVAYVDVVSKEVTRVIDTGVFPVPAEHGNYTDPELTGPLRTTQKPISITQPEGPSFTVTGGNHIEWEKWSLDVGFDVREGVVLHNIAFRDGDRLRPIINRASIAEMVVPYGDPSPIRSWQNYFDTGEYLVGQYANSLELGCDCLGDITYLSPVISDAFGNPREIRNGICMHEEDWGILAKHSDLWSGINYTRRNRRMVISFFTTIGNYDYGFYWYLYLDGTIEFEAKATGVVFTSAFPEGGSDNISQLAPGLGAPFHQHIFSARLDMAIDGFTNRVEEEDVVRQTMGPGNERGNAFSRKRTVLTRESEAVREADARTGRTWIISNPESKNRLNEPVGYKLHAHNQPTLLADPGSSIARRAAFATKDLWVTRYADDERYPTGDFVNQHSGGAGLPSYIAQDRDIDGQDIVVWHTFGLTHFPRVEDWPIMPVDTVGFKLRPEGFFDRSPVLDVPAN 628
               SCOP domains d2zl8a2 A:9-96 Copper amine oxidase, domains 1 and 2                                    d2zl8a3 A:97-211 Copper amine oxidase, domains 1 and 2                                                             d2zl8a1 A:212-628 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2zl8A01 A:9-95  [code=3.10.450.40, no name defined]                                    ------2zl8A02 A:102-203  [code=3.10.450.40, no name defined]                                                2zl8A03 A:204-627 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                                        - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh......eeeeeeee..............eeeeeeee......eeeeee....eeeeeee.hhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhh..hhh.eeeeeee.....hhhhh...eeeeeeee......hhhhh....eeeeee....eeeeeee..............hhhhhh.........eee.......eee...eeee..eeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeeeeee...........eee.....hhhhhh.............eee..eee.....eee....eeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..eeeeeeeeee....eeeeeeeee....ee........eeeee..eeee.eeeeeeeeeee.......eeeeeeeee............eeeeeeee.hhhh.ee..hhhhh.eeeeeeeeee.....eeeeeeee...........hhhhhhhhhhhh.eeeee....................hhhhhhh.........eeeeeeeeeee..hhhhh..eeeeeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zl8 A   9 ASPFRLASAGEISEVQGILRTAGLLGPEKRIAYLGVLDPARGAGSEAEDRRFRVFIHDVSGARPQEVTVSVTNGTVISAVELDTAATGELPVLEEEFEVVEQLLATDERWLKALAARNLDVSKVRVAPLSAGVFEYAEERGRRILRGLAFVQDFPEDSAWAHPVDGLVAYVDVVSKEVTRVIDTGVFPVPAEHGNYTDPELTGPLRTTQKPISITQPEGPSFTVTGGNHIEWEKWSLDVGFDVREGVVLHNIAFRDGDRLRPIINRASIAEMVVPYGDPSPIRSWQNYFDTGEYLVGQYANSLELGCDCLGDITYLSPVISDAFGNPREIRNGICMHEEDWGILAKHSDLWSGINYTRRNRRMVISFFTTIGNyDYGFYWYLYLDGTIEFEAKATGVVFTSAFPEGGSDNISQLAPGLGAPFHQHIFSARLDMAIDGFTNRVEEEDVVRQTMGPGNERGNAFSRKRTVLTRESEAVREADARTGRTWIISNPESKNRLNEPVGYKLHAHNQPTLLADPGSSIARRAAFATKDLWVTRYADDERYPTGDFVNQHSGGAGLPSYIAQDRDIDGQDIVVWHTFGLTHFPRVEDWPIMPVDTVGFKLRPEGFFDRSPVLDVPAN 628
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   |   388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628
                                                                                                                                                                                                                                                                                                                                                                                                               382-ESB

Chain B from PDB  Type:PROTEIN  Length:620
 aligned with PAOX_ARTGO | P46881 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:620
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628
           PAOX_ARTGO     9 ASPFRLASAGEISEVQGILRTAGLLGPEKRIAYLGVLDPARGAGSEAEDRRFRVFIHDVSGARPQEVTVSVTNGTVISAVELDTAATGELPVLEEEFEVVEQLLATDERWLKALAARNLDVSKVRVAPLSAGVFEYAEERGRRILRGLAFVQDFPEDSAWAHPVDGLVAYVDVVSKEVTRVIDTGVFPVPAEHGNYTDPELTGPLRTTQKPISITQPEGPSFTVTGGNHIEWEKWSLDVGFDVREGVVLHNIAFRDGDRLRPIINRASIAEMVVPYGDPSPIRSWQNYFDTGEYLVGQYANSLELGCDCLGDITYLSPVISDAFGNPREIRNGICMHEEDWGILAKHSDLWSGINYTRRNRRMVISFFTTIGNYDYGFYWYLYLDGTIEFEAKATGVVFTSAFPEGGSDNISQLAPGLGAPFHQHIFSARLDMAIDGFTNRVEEEDVVRQTMGPGNERGNAFSRKRTVLTRESEAVREADARTGRTWIISNPESKNRLNEPVGYKLHAHNQPTLLADPGSSIARRAAFATKDLWVTRYADDERYPTGDFVNQHSGGAGLPSYIAQDRDIDGQDIVVWHTFGLTHFPRVEDWPIMPVDTVGFKLRPEGFFDRSPVLDVPAN 628
               SCOP domains d2zl8b2 B:9-96 Copper amine oxidase, domains 1 and 2                                    d2zl8b3 B:97-211 Copper amine oxidase, domains 1 and 2                                                             d2zl8b1 B:212-628 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2zl8B01 B:9-95  [code=3.10.450.40, no name defined]                                    ------2zl8B02 B:102-203  [code=3.10.450.40, no name defined]                                                2zl8B03 B:204-627 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                                        - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------Cu_amine_oxidN3-2zl8B01 B:98-198                                                                     --------------------Cu_amine_oxid-2zl8B03 B:219-628                                                                                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------Cu_amine_oxidN3-2zl8B02 B:98-198                                                                     --------------------Cu_amine_oxid-2zl8B04 B:219-628                                                                                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhh......eeeeeeee..............eeeeeeee......eeeeee....eeeeeee.hhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhh..hhh.eeeeeee.....hhhhh...eeeeeeee......hhhhh....eeeeee....eeeeeee..............hhhhhh.........eee.......eee...eeee..eeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeeeeee...........eee.....hhhhhh.............eee..eee.....eee....eeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..eeeeeeeeee....eeeeeeeee....ee........eeeee..eeee.eeeeeeeeeee.......eeeeeeeee............eeeeeeee.hhhh.ee..hhhhh.eeeeeeeeee.....eeeeeeee...........hhhhhhhhhhhh.eeeee....................hhhhhhh.........eeeeeeeeeee..hhhhh..eeeeeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zl8 B   9 ASPFRLASAGEISEVQGILRTAGLLGPEKRIAYLGVLDPARGAGSEAEDRRFRVFIHDVSGARPQEVTVSVTNGTVISAVELDTAATGELPVLEEEFEVVEQLLATDERWLKALAARNLDVSKVRVAPLSAGVFEYAEERGRRILRGLAFVQDFPEDSAWAHPVDGLVAYVDVVSKEVTRVIDTGVFPVPAEHGNYTDPELTGPLRTTQKPISITQPEGPSFTVTGGNHIEWEKWSLDVGFDVREGVVLHNIAFRDGDRLRPIINRASIAEMVVPYGDPSPIRSWQNYFDTGEYLVGQYANSLELGCDCLGDITYLSPVISDAFGNPREIRNGICMHEEDWGILAKHSDLWSGINYTRRNRRMVISFFTTIGNyDYGFYWYLYLDGTIEFEAKATGVVFTSAFPEGGSDNISQLAPGLGAPFHQHIFSARLDMAIDGFTNRVEEEDVVRQTMGPGNERGNAFSRKRTVLTRESEAVREADARTGRTWIISNPESKNRLNEPVGYKLHAHNQPTLLADPGSSIARRAAFATKDLWVTRYADDERYPTGDFVNQHSGGAGLPSYIAQDRDIDGQDIVVWHTFGLTHFPRVEDWPIMPVDTVGFKLRPEGFFDRSPVLDVPAN 628
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   |   388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628
                                                                                                                                                                                                                                                                                                                                                                                                               382-ESB

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Supersandwich (271)

Superfamily: Amine oxidase catalytic domain (65)

Family: Amine oxidase catalytic domain (65)

Protein domain: Copper amine oxidase, domain 3 (62)

Arthrobacter globiformis [TaxId: 1665] (40)

1a	d2zl8a1	A:212-628
1b	d2zl8b1	B:212-628

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cystatin-like (403)

Superfamily: Amine oxidase N-terminal region (65)

Family: Amine oxidase N-terminal region (65)

Protein domain: Copper amine oxidase, domains 1 and 2 (62)

Arthrobacter globiformis [TaxId: 1665] (40)

2a	d2zl8a2	A:9-96
2b	d2zl8a3	A:97-211
2c	d2zl8b2	B:9-96
2d	d2zl8b3	B:97-211

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.40, no name defined] (77)

Arthrobacter globiformis. Organism_taxid: 1665. (34)

1a	2zl8A02	A:102-203
1b	2zl8B02	B:102-203
1c	2zl8A01	A:9-95
1d	2zl8B01	B:9-95

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Beta-galactosidase; Chain A, domain 5 (250)

Homologous Superfamily: Copper amine oxidase, Domain 3 (74)

Arthrobacter globiformis. Organism_taxid: 1665. (34)

2a	2zl8A03	A:204-627
2b	2zl8B03	B:204-627

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CuAO_N2_N3 (40)

Family: Cu_amine_oxidN3 (37)

Arthrobacter globiformis (13)

1a	Cu_amine_oxidN3-2zl8B01	B:98-198
1b	Cu_amine_oxidN3-2zl8B02	B:98-198

Clan: no clan defined [family: Cu_amine_oxid] (40)

Family: Cu_amine_oxid (40)

Arthrobacter globiformis (13)

2a	Cu_amine_oxid-2zl8B03	B:219-628
2b	Cu_amine_oxid-2zl8B04	B:219-628

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PAOX_ARTGO | P46881)

molecular function
	GO:0052595	aliphatic-amine oxidase activity	Catalysis of the reaction: an aliphatic amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide + H+.
	GO:0052594	aminoacetone:oxygen oxidoreductase(deaminating) activity	Catalysis of the reaction: aminoacetone + H2O + O2 = methylglyoxal + NH3 + hydrogen peroxide + H+.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0052596	phenethylamine:oxygen oxidoreductase (deaminating) activity	Catalysis of the reaction: phenylethylamine + O2 + H2O = phenylacetaldehyde + NH3 + hydrogen peroxide + H+.
	GO:0008131	primary amine oxidase activity	Catalysis of the reaction: a primary amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide.
	GO:0048038	quinone binding	Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
	GO:0052593	tryptamine:oxygen oxidoreductase (deaminating) activity	Catalysis of the reaction: tryptamine + H2O + O2 = NH3 + indole acetaldehyde + hydrogen peroxide + H+.
biological process
	GO:0009308	amine metabolic process	The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric/Biological Unit
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	2zl8
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1iu7	WILD-TYPE ENZYME (SUBSTRATE FREE)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (2, 6)

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