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(-) Description

Title :  X-RAY STRUCTURES AND MECHANISTIC IMPLICATIONS OF THREE FUNCTIONAL DERIVATIVES OF ASCORBATE OXIDASE FROM ZUCCHINI: REDUCED-, PEROXIDE-, AND AZIDE-FORMS
 
Authors :  A. Messerschmidt, H. Luecke, R. Huber
Date :  25 Nov 92  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Messerschmidt, H. Luecke, R. Huber
X-Ray Structures And Mechanistic Implications Of Three Functional Derivatives Of Ascorbate Oxidase From Zucchini. Reduced, Peroxide And Azide Forms.
J. Mol. Biol. V. 230 997 1993
PubMed-ID: 8478945  |  Reference-DOI: 10.1006/JMBI.1993.1215
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASCORBATE OXIDASE
    ChainsA, B
    EC Number1.10.3.3
    EngineeredYES
    Organism CommonZUCCHINI
    Organism ScientificCUCURBITA PEPO
    Organism Taxid3665
    StrainVAR. MELOPEPO

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1AZI4Ligand/IonAZIDE ION
2CU9Ligand/IonCOPPER (II) ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OH2Ligand/IonHYDROXIDE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1AZI4Ligand/IonAZIDE ION
2CU-1Ligand/IonCOPPER (II) ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OH-1Ligand/IonHYDROXIDE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1AZI8Ligand/IonAZIDE ION
2CU-1Ligand/IonCOPPER (II) ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4OH-1Ligand/IonHYDROXIDE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:71 , ASN A:92 , PRO A:532 , HOH A:956BINDING SITE FOR RESIDUE NAG A 553
02AC2SOFTWAREVAL B:45 , ASN B:92 , PRO B:532BINDING SITE FOR RESIDUE NAG B 553
03AC3SOFTWAREHIS A:445 , CYS A:507 , HIS A:512 , MET A:517BINDING SITE FOR RESIDUE CU A 554
04AC4SOFTWAREHIS A:106 , HIS A:450 , HIS A:506 , AZI A:559 , AZI A:560BINDING SITE FOR RESIDUE CU A 555
05AC5SOFTWAREHIS A:62 , HIS A:104 , HIS A:508 , CU A:557 , AZI A:560BINDING SITE FOR RESIDUE CU A 556
06AC6SOFTWAREHIS A:60 , HIS A:62 , HIS A:448 , HIS A:450 , CU A:556 , OH A:558BINDING SITE FOR RESIDUE CU A 557
07AC7SOFTWAREHIS A:60 , GLY A:63 , HIS A:448 , CU A:557 , HOH A:642 , HOH A:775BINDING SITE FOR RESIDUE OH A 558
08AC8SOFTWAREILE A:78 , HIS A:106 , HIS A:450 , ALA A:504 , HIS A:506 , CU A:555 , HOH A:702 , HOH A:707 , HOH A:816BINDING SITE FOR RESIDUE AZI A 559
09AC9SOFTWAREHIS A:104 , HIS A:106 , HIS A:450 , HIS A:506 , CU A:555 , CU A:556 , HOH A:646BINDING SITE FOR RESIDUE AZI A 560
10BC1SOFTWAREHIS B:445 , CYS B:507 , HIS B:512 , MET B:517BINDING SITE FOR RESIDUE CU B 554
11BC2SOFTWAREHIS B:106 , HIS B:450 , HIS B:506 , AZI B:559 , AZI B:560BINDING SITE FOR RESIDUE CU B 555
12BC3SOFTWAREHIS B:62 , HIS B:104 , HIS B:508 , CU B:557 , AZI B:560BINDING SITE FOR RESIDUE CU B 556
13BC4SOFTWAREHIS B:60 , HIS B:62 , HIS B:448 , HIS B:450 , CU B:556 , OH B:558BINDING SITE FOR RESIDUE CU B 557
14BC5SOFTWAREHIS B:60 , HIS B:62 , GLY B:63 , HIS B:448 , CU B:557 , HOH B:661BINDING SITE FOR RESIDUE OH B 558
15BC6SOFTWAREILE B:78 , HIS B:106 , HIS B:450 , ALA B:504 , HIS B:506 , CU B:555 , HOH B:725BINDING SITE FOR RESIDUE AZI B 559
16BC7SOFTWAREHIS B:104 , HIS B:106 , HIS B:450 , HIS B:506 , HIS B:508 , CU B:555 , CU B:556BINDING SITE FOR RESIDUE AZI B 560
17BC8SOFTWAREHIS A:286 , HIS B:286BINDING SITE FOR RESIDUE CU A 561

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:19 -A:201
2A:81 -A:538
3A:180 -A:193
4B:19 -B:201
5B:81 -B:538
6B:180 -B:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:31 -Pro A:32
2Lys A:159 -Pro A:160
3Leu A:299 -Pro A:300
4Phe B:31 -Pro B:32
5Lys B:159 -Pro B:160
6Leu B:299 -Pro B:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.ASO_CUCPM501-521
 
  2A:501-521
B:501-521
2MULTICOPPER_OXIDASE2PS00080 Multicopper oxidases signature 2.ASO_CUCPM506-517
 
  2A:506-517
B:506-517
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.ASO_CUCPM501-521
 
  2A:501-521
B:501-521
2MULTICOPPER_OXIDASE2PS00080 Multicopper oxidases signature 2.ASO_CUCPM506-517
 
  2A:506-517
B:506-517
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.ASO_CUCPM501-521
 
  4A:501-521
B:501-521
2MULTICOPPER_OXIDASE2PS00080 Multicopper oxidases signature 2.ASO_CUCPM506-517
 
  4A:506-517
B:506-517

(-) Exons   (0, 0)

(no "Exon" information available for 1ASQ)

(-) 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:552
 aligned with ASO_CUCPM | P37064 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:552
                                    10        20        30        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  
            ASO_CUCPM     1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
               SCOP domains d1asqa1 A:1-129 Ascorbate oxidase                                                                                                d1asqa2 A:130-338 Ascorbate oxidase                                                                                                                                                                              d1asqa3 A:339-552 Ascorbate oxidase                                                                                                                                                                                    SCOP domains
               CATH domains 1asqA01 A:1-130 Cupredoxins -  blue copper proteins                                                                               1asqA02 A:131-336 Cupredoxins -  blue copper proteins                                                                                                                                                         1asqA03 A:337-552 Cupredoxins -  blue copper proteins                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeeeee........eeee...eeeeeeee........eeee......hhhhh..............eeeeeee....eeeeeee...hhhhhh.eeeeeee............eeeeeeeeee...hhhhhhhhh............eeee..........hhhhh..................eee....eeeeeeee.....eeeeee....eeeeee..eeeeeeee..eee....eeeeeee........eeeeeeee........eeeeeee....................hhhhhhhhhhh...............eeeeeeeeeeee..eeeeee..eee.....hhhhhhhh..............................eee...eee....eeeeeee............eeeee....eeeeeeee...hhhhhhhh......ee.eeee...eeeeeeee....eeeeeee.hhhhhhh..eeeeee.hhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_----------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1asq A   1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
                                    10        20        30        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  

Chain B from PDB  Type:PROTEIN  Length:552
 aligned with ASO_CUCPM | P37064 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:552
                                    10        20        30        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  
            ASO_CUCPM     1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
               SCOP domains d1asqb1 B:1-129 Ascorbate oxidase                                                                                                d1asqb2 B:130-338 Ascorbate oxidase                                                                                                                                                                              d1asqb3 B:339-552 Ascorbate oxidase                                                                                                                                                                                    SCOP domains
               CATH domains 1asqB01 B:1-130 Cupredoxins -  blue copper proteins                                                                               1asqB02 B:131-336 Cupredoxins -  blue copper proteins                                                                                                                                                         1asqB03 B:337-552 Cupredoxins -  blue copper proteins                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeeeee........eeee...eeeeeeee........eeee......hhhhh..............eeeeeee....eeeeeee...hhhhhh.eeeeeee............eeeeeeeeee...hhhhhhhhhhh..........eeee..........hhhhh..................eee....eeeeeeee.....eeeeee....eeeeee..eeeeeeee.eeee....eeeeeee........eeeeeeee........eeeeeee....................hhhhhhhhhh................eeeeeeeeeeee..eeeeee..eee.....hhhhhhhh..............................eee...eee....eeeeeee............eeeee....eeeeeeee...hhhhhhhh......ee.eeee...eeeeeeee....eeeeeee.hhhhhhh..eeeeee.hhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_----------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1asq B   1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
                                    10        20        30        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  

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ASO_CUCPM | P37064)
molecular function
    GO:0008447    L-ascorbate oxidase activity    Catalysis of the reaction: 2 L-ascorbate + O2 = 2 dehydroascorbate + 2 H2O.
    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.
biological process
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ASO_CUCPM | P370641aoz 1aso 1asp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ASQ)