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(-) Description

Title :  CRYSTAL STRUCTURE OF A EUKARYOTIC (PEA SEEDLING) COPPER-CONTAINING AMINE OXIDASE AT 2.2A RESOLUTION
 
Authors :  M. C. J. Wilce, V. Kumar, H. C. Freeman, J. M. Guss
Date :  20 Jul 96  (Deposition) - 24 Dec 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidase, Pea Seedling, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Kumar, D. M. Dooley, H. C. Freeman, J. M. Guss, I. Harvey, M. A. Mcguirl, M. C. Wilce, V. M. Zubak
Crystal Structure Of A Eukaryotic (Pea Seedling) Copper-Containing Amine Oxidase At 2. 2 A Resolution.
Structure V. 4 943 1996
PubMed-ID: 8805580  |  Reference-DOI: 10.1016/S0969-2126(96)00101-3

(-) Compounds

Molecule 1 - COPPER AMINE OXIDASE
    ChainsA, B
    EC Number1.4.3.6
    Organism CommonPEA
    Organism ScientificPISUM SATIVUM
    Organism Taxid3888

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2MN2Ligand/IonMANGANESE (II) ION
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4TPQ2Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:131 , SER A:133 , GLU A:134 , NAG A:656BINDING SITE FOR RESIDUE NAG A 655
02AC2SOFTWARENAG A:655BINDING SITE FOR RESIDUE NAG A 656
03AC3SOFTWAREASN A:558 , THR A:560 , GLU A:561 , GLN A:584BINDING SITE FOR RESIDUE NAG A 657
04AC4SOFTWAREASN B:131 , SER B:133 , GLU B:134 , NAG B:656BINDING SITE FOR RESIDUE NAG B 655
05AC5SOFTWARENAG B:655BINDING SITE FOR RESIDUE NAG B 656
06AC6SOFTWAREASN B:558 , THR B:560 , GLU B:561 , GLN B:584BINDING SITE FOR RESIDUE NAG B 657
07AC7SOFTWAREHIS A:442 , HIS A:444 , HIS A:603 , HOH A:658 , HOH A:659BINDING SITE FOR RESIDUE CU A 650
08AC8SOFTWAREASP A:451 , PHE A:452 , ASP A:453 , ASP A:592 , ILE A:593 , HOH A:660BINDING SITE FOR RESIDUE MN A 653
09AC9SOFTWAREHIS B:442 , HIS B:444 , HIS B:603 , HOH B:658 , HOH B:659BINDING SITE FOR RESIDUE CU B 650
10ACAUNKNOWNHIS A:442 , HIS A:444 , HIS A:603 , CU A:650 , HOH A:658 , HOH A:659 , TPQ A:387THE COPPER ATOM IN THE ACTIVE SITE OF EACH SUBUNIT IS LIGATED TO THREE HISTIDINE RESIDUES AND TWO WATER MOLECULES IN A DISTORTED SQUARE PYRAMIDAL ARRANGEMENT. THE ORGANIC COFACTOR TOPA QUINONE (TPQ) IS IN THE ACTIVE SITE WITH THE NEAREST QUINONE OXYGEN ATOM AT ~6A FROM THE COPPER ATOM.
11ACBUNKNOWNHIS B:442 , HIS B:444 , HIS B:603 , CU B:650 , HOH B:658 , HOH B:659 , TPQ B:387THE COPPER ATOM IN THE ACTIVE SITE OF EACH SUBUNIT IS LIGATED TO THREE HISTIDINE RESIDUES AND TWO WATER MOLECULES IN A DISTORTED SQUARE PYRAMIDAL ARRANGEMENT. THE ORGANIC COFACTOR TOPA QUINONE (TPQ) IS IN THE ACTIVE SITE WITH THE NEAREST QUINONE OXYGEN ATOM AT ~6A FROM THE COPPER ATOM.
12BC1SOFTWAREASP B:451 , PHE B:452 , ASP B:453 , ASP B:592 , ILE B:593 , HOH B:660BINDING SITE FOR RESIDUE MN B 653

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:137 -A:158
2A:319 -A:345
3B:137 -B:158
4B:319 -B:345

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:212 -Pro A:213
2Gly A:215 -Pro A:216
3Phe A:610 -Pro A:611
4Pro B:212 -Pro B:213
5Gly B:215 -Pro B:216
6Phe B:610 -Pro B:611

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_AMINE_OXID_1PS01164 Copper amine oxidase topaquinone signature.AMO_PEA401-414
 
  2A:376-389
B:376-389

(-) Exons   (0, 0)

(no "Exon" information available for 1KSI)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:642
 aligned with AMO_PEA | Q43077 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:642
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670  
              AMO_PEA    31 VQHPLDPLTKEEFLAVQTIVQNKYPISNNRLAFHYIGLDDPEKDHVLRYETHPTLVSIPRKIFVVAIINSQTHEILINLRIRSIVSDNIHNGYGFPILSVDEQSLAIKLPLKYPPFIDSVKKRGLNLSEIVCSSFTMGWFGEEKNVRTVRLDCFMKESTVNIYVRPITGITIVADLDLMKIVEYHDRDIEAVPTAENTEYQVSKQSPPFGPKQHSLTSHQPQGPGFQINGHSVSWANWKFHIGFDVRAGIVISLASIYDLEKHKSRRVLYKGYISELFVPYQDPTEEFYFKTFFDSGEFGFGLSTVSLIPNRDCPPHAQFIDTYVHSANGTPILLKNAICVFEQYGNIMWRHTENGIPNESIEESRTEVNLIVRTIVTVGNYDNVIDWEFKASGSIKPSIALSGILEIKGTNIKHKDEIKEDLHGKLVSANSIGIYHDHFYIYYLDFDIDGTHNSFEKTSLKTVRIKDGSSKRKSYWTTETQTAKTESDAKITIGLAPAELVVVNPNIKTAVGNEVGYRLIPAIPAHPLLTEDDYPQIRGAFTNYNVWVTAYNRTEKWAGGLYVDHSRGDDTLAVWTKQNREIVNKDIVMWHVVGIHHVPAQEDFPIMPLLSTSFELRPTNFFERNPVLKTLSPRDVAWPGC 672
               SCOP domains d1ksia2 A:6-98 Copper amine oxidase, domains 1 and 2                                         d1ksia3 A:99-206 Copper amine oxidase, domains 1 and 2                                                      d1ksia1 A:207-647 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ksiA01 A:6-101  [code=3.10.450.40, no name defined]                                            1ksiA02 A:102-197  [code=3.10.450.40, no name defined]                                          ---------------------------------1ksiA03 A:231-646 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                                - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhh.hhh.....eeeeeeee..eeeeeeee....eeeeeee..........hhhhhhhhhhhhh.hhhhhhhhh....hhheeeeee............eeeeeeee......hhh.....eeeeee....eeeeeee.......................................eeee..eeee..eeeeeeee...eeeee.eeeee....eeeeeeeeeee.eee................hhhhh...................eee.eeee.....eeee...eeeeee..eeeeeeee.......eeeeeee.eeeeeeee......eeeeeeee....eeeeeee.....eee.....hhh......eeeee..eeee.eeeeeeeeeee.......eeeeeeeeeee.........eeeeeeeee...hhhh........eeeeeeeeeee.....eeeeeee.............hhhhh.hhhh..eeeee.....................hhhhhhh........eeeeeeeeeee...hhh......eeee.eeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ksi A   6 VQHPLDPLTKEEFLAVQTIVQNKYPISNNRLAFHYIGLDDPEKDHVLRYETHPTLVSIPRKIFVVAIINSQTHEILINLRIRSIVSDNIHNGYGFPILSVDEQSLAIKLPLKYPPFIDSVKKRGLNLSEIVCSSFTMGWFGEEKNVRTVRLDCFMKESTVNIYVRPITGITIVADLDLMKIVEYHDRDIEAVPTAENTEYQVSKQSPPFGPKQHSLTSHQPQGPGFQINGHSVSWANWKFHIGFDVRAGIVISLASIYDLEKHKSRRVLYKGYISELFVPYQDPTEEFYFKTFFDSGEFGFGLSTVSLIPNRDCPPHAQFIDTYVHSANGTPILLKNAICVFEQYGNIMWRHTENGIPNESIEESRTEVNLIVRTIVTVGNyDNVIDWEFKASGSIKPSIALSGILEIKGTNIKHKDEIKEDLHGKLVSANSIGIYHDHFYIYYLDFDIDGTHNSFEKTSLKTVRIKDGSSKRKSYWTTETQTAKTESDAKITIGLAPAELVVVNPNIKTAVGNEVGYRLIPAIPAHPLLTEDDYPQIRGAFTNYNVWVTAYNRTEKWAGGLYVDHSRGDDTLAVWTKQNREIVNKDIVMWHVVGIHHVPAQEDFPIMPLLSTSFELRPTNFFERNPVLKTLSPRDVAWPGC 647
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385 |     395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645  
                                                                                                                                                                                                                                                                                                                                                                                                                       387-TPQ                                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:642
 aligned with AMO_PEA | Q43077 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:642
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670  
              AMO_PEA    31 VQHPLDPLTKEEFLAVQTIVQNKYPISNNRLAFHYIGLDDPEKDHVLRYETHPTLVSIPRKIFVVAIINSQTHEILINLRIRSIVSDNIHNGYGFPILSVDEQSLAIKLPLKYPPFIDSVKKRGLNLSEIVCSSFTMGWFGEEKNVRTVRLDCFMKESTVNIYVRPITGITIVADLDLMKIVEYHDRDIEAVPTAENTEYQVSKQSPPFGPKQHSLTSHQPQGPGFQINGHSVSWANWKFHIGFDVRAGIVISLASIYDLEKHKSRRVLYKGYISELFVPYQDPTEEFYFKTFFDSGEFGFGLSTVSLIPNRDCPPHAQFIDTYVHSANGTPILLKNAICVFEQYGNIMWRHTENGIPNESIEESRTEVNLIVRTIVTVGNYDNVIDWEFKASGSIKPSIALSGILEIKGTNIKHKDEIKEDLHGKLVSANSIGIYHDHFYIYYLDFDIDGTHNSFEKTSLKTVRIKDGSSKRKSYWTTETQTAKTESDAKITIGLAPAELVVVNPNIKTAVGNEVGYRLIPAIPAHPLLTEDDYPQIRGAFTNYNVWVTAYNRTEKWAGGLYVDHSRGDDTLAVWTKQNREIVNKDIVMWHVVGIHHVPAQEDFPIMPLLSTSFELRPTNFFERNPVLKTLSPRDVAWPGC 672
               SCOP domains d1ksib2 B:6-98 Copper amine oxidase, domains 1 and 2                                         d1ksib3 B:99-206 Copper amine oxidase, domains 1 and 2                                                      d1ksib1 B:207-647 Copper amine oxidase, domain 3                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ksiB01 B:6-101  [code=3.10.450.40, no name defined]                                            1ksiB02 B:102-197  [code=3.10.450.40, no name defined]                                          ---------------------------------1ksiB03 B:231-646 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                                - CATH domains
           Pfam domains (1) --Cu_amine_oxidN2-1ksiB01 B:8-95                                                          -----Cu_amine_oxidN3-1ksiB03 B:101-198                                                                 ---------------------Cu_amine_oxid-1ksiB05 B:220-641                                                                                                                                                                                                                                                                                                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) --Cu_amine_oxidN2-1ksiB02 B:8-95                                                          -----Cu_amine_oxidN3-1ksiB04 B:101-198                                                                 ---------------------Cu_amine_oxid-1ksiB06 B:220-641                                                                                                                                                                                                                                                                                                                                                                                                       ------ Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhh.hhh.....eeeeeeee..eeeeeeee....eeeeeee..........hhhhhhhhhhhhh.hhhhhhhhh....hhheeeeee............eeeeeeee......hhh.....eeeeee....eeeeeee...............hhh.....................eeee..eeee..eeeeeeee...eeeee.eeeee....eeeeeeeeeee.eee................hhhhh...................eee.eeee.....eeee...eeeeee..eeeeeeee.......eeeeeee.eeeeeeee......eeeeeee.....eeeeeee.....eee.....hhh......eeeee..eeee.eeeeeeeeeee.......eeeeeeeeeee.........eeeeeeeee...............eeeeeeeeeee.....eeeeeee.............hhhhh.hhhh..eeeee.....................hhhhhhh........eeeeeeeeeee...hhh......eeee.eeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPPER_AMINE_O------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ksi B   6 VQHPLDPLTKEEFLAVQTIVQNKYPISNNRLAFHYIGLDDPEKDHVLRYETHPTLVSIPRKIFVVAIINSQTHEILINLRIRSIVSDNIHNGYGFPILSVDEQSLAIKLPLKYPPFIDSVKKRGLNLSEIVCSSFTMGWFGEEKNVRTVRLDCFMKESTVNIYVRPITGITIVADLDLMKIVEYHDRDIEAVPTAENTEYQVSKQSPPFGPKQHSLTSHQPQGPGFQINGHSVSWANWKFHIGFDVRAGIVISLASIYDLEKHKSRRVLYKGYISELFVPYQDPTEEFYFKTFFDSGEFGFGLSTVSLIPNRDCPPHAQFIDTYVHSANGTPILLKNAICVFEQYGNIMWRHTENGIPNESIEESRTEVNLIVRTIVTVGNyDNVIDWEFKASGSIKPSIALSGILEIKGTNIKHKDEIKEDLHGKLVSANSIGIYHDHFYIYYLDFDIDGTHNSFEKTSLKTVRIKDGSSKRKSYWTTETQTAKTESDAKITIGLAPAELVVVNPNIKTAVGNEVGYRLIPAIPAHPLLTEDDYPQIRGAFTNYNVWVTAYNRTEKWAGGLYVDHSRGDDTLAVWTKQNREIVNKDIVMWHVVGIHHVPAQEDFPIMPLLSTSFELRPTNFFERNPVLKTLSPRDVAWPGC 647
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385 |     395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645  
                                                                                                                                                                                                                                                                                                                                                                                                                       387-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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AMO_PEA | Q43077)
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:0052597    diamine oxidase activity    Catalysis of the reaction: a diamine + H2O + O2 = a monoamine + NH3 + hydrogen peroxide.
    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:0097185    cellular response to azide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an azide stimulus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMO_PEA | Q430771w2z

(-) Related Entries Specified in the PDB File

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