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(-) Description

Title :  AGAO IN COMPLEX WITH RUTHENIUM-C4-WIRE AT 1.73 ANGSTROMS
 
Authors :  D. B. Langley, A. P. Duff, H. C. Freeman, J. M. Guss, G. A. Juda, D. M. Doole S. M. Contakes, N. W. Halpern-Manners, A. R. Dunn, H. B. Gray
Date :  26 May 05  (Deposition) - 05 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Amine Oxidase, Arthrobacter Globiformis, Copper Containing, Oxidoreductase, Tpq, Quinone, Ruthenium Diimine Wires, Competitive Inhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Contakes, G. A. Juda, D. B. Langley, N. W. Halpern-Manners, A. P. Duff, A. R. Dunn, H. B. Gray, D. M. Dooley, J. M. Guss, H. C. Freeman
Reversible Inhibition Of Copper Amine Oxidase Activity By Channel-Blocking Ruthenium(Ii) And Rhenium(I) Molecular Wires.
Proc. Natl. Acad. Sci. Usa V. 102 13451 2005
PubMed-ID: 16157884  |  Reference-DOI: 10.1073/PNAS.0506336102

(-) Compounds

Molecule 1 - PHENYLETHYLAMINE OXIDASE
    Chains: A
    EC Number: 1.4.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAGAO2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-3C (NOVAGEN)
    Fragment: AGAO HOLOENZYME, RESIDUES 3-638
    Organism Scientific: ARTHROBACTER GLOBIFORMIS
    Organism Taxid: 1665
    Other Details: RESIDUE A382 WAS AN ACTIVE SITE TYROSINE RESIDUE, WHICH WAS AUTOCATALYTICALLY MODIFIED TO BECOME TPQ
    Synonym: AMINE OXIDASE, COPPER AMINE OXIDASE

 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, 13)

Asymmetric Unit (6, 13)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2GOL6Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4R4A1Ligand/IonBIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~]{3-[4-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)BUTOXY]-N,N-DIMETHYLANILINATO(2-)}RUTHENIUM
5SO43Ligand/IonSULFATE ION
6TPQ1Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
Biological Unit 1 (4, 22)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2GOL12Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4R4A2Ligand/IonBIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~]{3-[4-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)BUTOXY]-N,N-DIMETHYLANILINATO(2-)}RUTHENIUM
5SO46Ligand/IonSULFATE ION
6TPQ2Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:431 , HIS A:433 , HIS A:592 , HOH A:2290 , HOH A:2328BINDING SITE FOR RESIDUE CU A1629
02AC2SOFTWAREASP A:440 , MET A:441 , ASP A:581 , ILE A:582 , HOH A:2334BINDING SITE FOR RESIDUE NA A1630
03AC3SOFTWAREASP A:316 , CYS A:317 , LEU A:318 , HIS A:345 , GLY A:350 , ARG A:367 , GOL A:1639 , HOH A:2292 , HOH A:2293 , HOH A:2496 , HOH A:2497BINDING SITE FOR RESIDUE SO4 A1632
04AC4SOFTWARETHR A:233 , GLY A:234 , HOH A:2498BINDING SITE FOR RESIDUE SO4 A1633
05AC5SOFTWAREARG A:545 , HOH A:2456 , HOH A:2499BINDING SITE FOR RESIDUE SO4 A1634
06AC6SOFTWAREGLU A:102 , PHE A:105 , ALA A:135 , PRO A:136 , LEU A:137 , TRP A:168 , TYR A:296 , TYR A:302 , GLN A:306 , TYR A:307 , ASN A:309 , ARG A:336 , SER A:356 , ASP A:357 , LEU A:358 , THR A:378 , ILE A:379 , GLY A:380 , ASN A:381 , TPQ A:382 , HOH A:2289BINDING SITE FOR RESIDUE R4A A1631
07AC7SOFTWAREARG 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:2436BINDING SITE FOR RESIDUE GOL A1635
08AC8SOFTWAREASN A:126 , ASP A:161 , VAL A:197 , ALA A:199 , HOH A:2500 , HOH A:2501 , HOH A:2502BINDING SITE FOR RESIDUE GOL A1636
09AC9SOFTWAREASP A:605 , LYS A:610 , HOH A:2468BINDING SITE FOR RESIDUE GOL A1637
10BC1SOFTWARELEU A:209 , THR A:210 , SER A:620 , PRO A:621 , VAL A:622 , LEU A:623 , ASP A:624 , HOH A:2504BINDING SITE FOR RESIDUE GOL A1638
11BC2SOFTWAREGLU A:347 , TRP A:349 , ARG A:370 , LYS A:401 , SO4 A:1632 , HOH A:2265 , HOH A:2267 , HOH A:2303 , HOH A:2497 , HOH A:2505 , HOH A:2506BINDING SITE FOR RESIDUE GOL A1639
12BC3SOFTWAREASN A:368 , ASP A:393 , LYS A:610 , HOH A:2287 , HOH A:2476 , HOH A:2479 , HOH A:2507 , HOH A:2508BINDING SITE FOR RESIDUE GOL A1640

(-) 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 2BT3)

(-) 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 2BT3)

(-) 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 d2bt3a2 A:9-96 Copper amine oxidase, domains 1 and 2                                    d2bt3a3 A:97-211 Copper amine oxidase, domains 1 and 2                                                             d2bt3a1 A:212-628 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bt3A01 A:9-95  [code=3.10.450.40, no name defined]                                    ------2bt3A02 A:102-203  [code=3.10.450.40, no name defined]                                                2bt3A03 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.....hhhhh..............eee..eee.....eee....eeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..eeeeeeeeee....eeeeeeeee....ee........eeeee..eeee.eeeeeeeeeee.......eeeeeeeee............eeeeeeee..hhh.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
                 2bt3 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 2BT3)

(-) 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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  2bt3
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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 1rjo 1sih 1sii 1ui7 1ui8 1w4n 1w5z 1w6c 1w6g 1wmn 1wmo 1wmp 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 CRYSTAL STRUCTURES OF THE COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS IN THE HOLO- AND APO-FORMS: IMPLICATIONS FOR THE BIOGENESIS OF TOPA QUINONE
1avk CRYSTAL STRUCTURES OF THE COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS IN THE HOLO- AND APO-FORMS: IMPLICATIONS FOR THE BIOGENESIS OF TOPA QUINONE
1avl CRYSTAL STRUCTURES OF THE COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS IN THE HOLO- AND APO-FORMS: IMPLICATIONS FOR THE BIOGENESIS OF TOPA QUINONE
1iqx CRYSTAL STRUCTURE OF COBALT-SUBSTITUTED AMINE OXIDASE FROMARTHROBACTER GLOBIFORMIS
1iqy CRYSTAL STRUCTURE OF NICKEL-SUBSTITUTED AMINE OXIDASE FROMARTHROBACTER GLOBIFORMIS
1iu7 HOLO FORM OF COPPER-CONTAINING AMINE OXIDASE FROMARTHROBACTER GLOBIFORMIS
1ivu CRYSTAL STRUCTURE OF COPPER AMINE OXIDASE FROM ARTHROBACTERGLOBIFORMIS: INITIAL INTERMEDIATE IN TOPAQUINONE BIOGENESIS
1ivv CRYSTAL STRUCTURE OF COPPER AMINE OXIDASE FROM ARTHROBACTERGLOBIFORMIS: EARLY INTERMEDIATE IN TOPAQUINONE BIOGENESIS
1ivw CRYSTAL STRUCTURE OF COPPER AMINE OXIDASE FROM ARTHROBACTERGLOBIFORMIS: LATE INTERMEDIATE IN TOPAQUINONE BIOGENESIS
1ivx CRYSTAL STRUCTURE OF COPPER AMINE OXIDASE FROM ARTHROBACTERGLOBIFORMIS: HOLO FORM GENERATED BY BIOGENESIS IN CRYSTAL.
1rjo AGAO + XE
1sih AGAO IN COVALENT COMPLEX WITH THE INHIBITOR MOBA ("4-(4-METHYLPHENOXY)-2-BUTYN-1- AMINE")
1sii AGAO IN COVALENT COMPLEX WITH THE INHIBITOR NOBA ("4-(2-NAPHTHYLOXY)-2-BUTYN-1-AMINE ")
1ui7 SITE-DIRECTED MUTAGENESIS OF HIS433 INVOLVED IN BINDING OFCOPPER ION IN ARTHROBACTER GLOBIFORMIS AMINE OXIDASE
1ui8 SITE-DIRECTED MUTAGENESIS OF HIS592 INVOLVED IN BINDING OFCOPPER ION IN ARTHROBACTER GLOBIFORMIS AMINE OXIDASE
1w4n AGAO COVALENT COMPLEX WITH TRANYLCYPROMINE
1w5z AGAO COVALENT COMPLEX WITH BENZYLHYDRAZINE
1w6c AGAO HOLOENZYME IN A SMALL CELL, AT 2.2 ANGSTROMS
1w6g AGAO HOLOENZYME AT 1.55 ANGSTROMS