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(-) Description

Title :  AGAO + XE
 
Authors :  J. M. Guss, D. M. Trambaiolo, A. P. Duff
Date :  19 Nov 03  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cao, Cuao, Copper-Containing, Amine Oxidase, Oxygen Binding Site, Dioxygen Binding Site, Xenon, Tpq, Quinone, Trihydroxyphenylalanine Quinone, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Duff, D. M. Trambaiolo, A. E. Cohen, P. J. Ellis, G. A. Juda, E. M. Shepard, D. B. Langley, D. M. Dooley, H. C. Freeman, J. M. Guss
Using Xenon As A Probe For Dioxygen-Binding Sites In Copper Amine Oxidases
J. Mol. Biol. V. 344 599 2004
PubMed-ID: 15533431  |  Reference-DOI: 10.1016/J.JMB.2004.09.075

(-) Compounds

Molecule 1 - PHENYLETHYLAMINE OXIDASE
    Chains: A
    EC Number: 1.4.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PAGAO2
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTHROBACTER GLOBIFORMIS
    Organism Taxid: 1665
    Synonym: AMINE OXIDASE, COPPER AMINE OXIDASE, AGAO

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2GOL3Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
5TPQ1Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
6XE7Ligand/IonXENON
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2GOL6Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION
5TPQ2Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
6XE-1Ligand/IonXENON

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:431 , HIS A:433 , HIS A:592 , HOH A:1745BINDING SITE FOR RESIDUE CU A 701
02AC2SOFTWAREASP A:440 , MET A:441 , ASP A:581 , ILE A:582 , HOH A:1219BINDING SITE FOR RESIDUE NA A 703
03AC3SOFTWAREASP A:316 , CYS A:317 , LEU A:318 , HIS A:345 , GLY A:350 , ARG A:367 , TYR A:387 , HOH A:1234 , HOH A:1428 , HOH A:1518 , HOH A:1606BINDING SITE FOR RESIDUE SO4 A 1101
04AC4SOFTWAREILE A:238 , LEU A:245 , LEU A:390BINDING SITE FOR RESIDUE XE A 901
05AC5SOFTWAREALA A:402 , LEU A:590BINDING SITE FOR RESIDUE XE A 902
06AC6SOFTWAREARG A:71BINDING SITE FOR RESIDUE XE A 903
07AC7SOFTWAREILE A:373 , TRP A:388 , LEU A:390BINDING SITE FOR RESIDUE XE A 904
08AC8SOFTWAREVAL A:23 , GLN A:24 , ILE A:39 , LEU A:42 , GLY A:333BINDING SITE FOR RESIDUE XE A 905
09AC9SOFTWARELEU A:42 , VAL A:327BINDING SITE FOR RESIDUE XE A 909
10BC1SOFTWARETRP A:359 , HOH A:1746BINDING SITE FOR RESIDUE XE A 910
11BC2SOFTWAREARG A:532 , ARG A:533 , THR A:554 , PHE A:557 , HIS A:561 , SER A:562 , GLY A:563 , GLY A:564 , ALA A:565 , HOH A:1256BINDING SITE FOR RESIDUE GOL A 1201
12BC3SOFTWAREASN A:126 , ASP A:161 , VAL A:197 , ALA A:199 , HOH A:1475 , HOH A:1493 , HOH A:1563BINDING SITE FOR RESIDUE GOL A 1202
13BC4SOFTWAREASP A:444 , GLY A:445 , PHE A:446 , THR A:447 , ASN A:499BINDING SITE FOR RESIDUE GOL A 1203

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:317 -A:343

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:599 -Pro A:600

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RJO)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_AMINE_OXID_1PS01164 Copper amine oxidase topaquinone signature.PAOX_ARTGO371-384  1A:371-384
2COPPER_AMINE_OXID_2PS01165 Copper amine oxidase copper-binding site signature.PAOX_ARTGO587-600  1A:587-600
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_AMINE_OXID_1PS01164 Copper amine oxidase topaquinone signature.PAOX_ARTGO371-384  2A:371-384
2COPPER_AMINE_OXID_2PS01165 Copper amine oxidase copper-binding site signature.PAOX_ARTGO587-600  2A:587-600

(-) Exons   (0, 0)

(no "Exon" information available for 1RJO)

(-) Sequences/Alignments

Asymmetric 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
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 d1rjoa2 A:9-96 Copper amine oxidase, domains 1 and 2                                    d1rjoa3 A:97-211 Copper amine oxidase, domains 1 and 2                                                             d1rjoa1 A:212-628 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1rjoA01 A:9-95  [code=3.10.450.40, no name defined]                                    ------1rjoA02 A:102-203  [code=3.10.450.40, no name defined]                                                1rjoA03 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......hhhh.eeeeeeeeee....eeeeeee..............hhhhhh...................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
                 1rjo 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-TPQ
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RJO)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

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  1rjo
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  PAOX_ARTGO | P46881
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  1.4.3.6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PAOX_ARTGO | P46881: 1av4 1avk 1avl 1iqx 1iqy 1iu7 1ivu 1ivv 1ivw 1ivx 1sih 1sii 1ui7 1ui8 1w4n 1w5z 1w6c 1w6g 1wmn 1wmo 1wmp 2bt3 2cfd 2cfg 2cfk 2cfl 2cfw 2cg0 2cg1 2cwt 2cwu 2cwv 2d1w 2e2t 2e2u 2e2v 2yx9 2zl8 3amo 3kii 3kn4 3wa2 3wa3 3x3x 3x3y 3x3z 3x40 3x41 3x42

(-) Related Entries Specified in the PDB File

1av4 AGAO