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(-) Description

Title :  CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE
 
Authors :  T. Klabunde, C. Eicken, J. C. Sacchettini, B. Krebs
Date :  02 Sep 98  (Deposition) - 02 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Catechol Oxidase, Dicopper Enzyme, Ipomoea Batatas, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Klabunde, C. Eicken, J. C. Sacchettini, B. Krebs
Crystal Structure Of A Plant Catechol Oxidase Containing A Dicopper Center.
Nat. Struct. Biol. V. 5 1084 1998
PubMed-ID: 9846879  |  Reference-DOI: 10.1038/4193
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CATECHOL OXIDASE)
    Chains: A
    EC Number: 1.10.3.1
    Organ: MATURE TUBER
    Organism Common: SWEET POTATO
    Organism Scientific: IPOMOEA BATATAS
    Organism Taxid: 4120
    Other Details: COVALENT THIOETHER BOND BETWEEN H109 AND C92
    Synonym: O-DIPHENOL OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1C2O1Ligand/IonCU-O-CU LINKAGE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:88 , HIS A:109 , HIS A:118 , HIS A:240 , HIS A:244 , HIS A:274BINDING SITE FOR RESIDUE C2O A 500
2CUAAUTHORHIS A:88 , HIS A:109 , HIS A:118BINDING SITE FOR COPPER A
3CUBAUTHORHIS A:240 , HIS A:244 , HIS A:274BINDING SITE FOR COPPER B

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:28
2A:27 -A:89

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BT3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYROSINASE_1PS00497 Tyrosinase CuA-binding region signature.PPO1_IPOBA109-126  1A:109-126

(-) Exons   (0, 0)

(no "Exon" information available for 1BT3)

(-) Sequences/Alignments

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
(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:336
 aligned with PPO1_IPOBA | Q9ZP19 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:341
                                    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 
           PPO1_IPOBA     1 APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLAGKPRKRDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWL 341
               SCOP domains d1bt3a_ A: Catechol oxidase                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1bt3A00 A:1-341 Di-copper center containing domain from catechol oxidase                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh........................eee.........eee..hhh..hhhhhhhhhhhhhhh.........hhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhh..............hhh....hhhh............hhh..................hhhhhhhhhhhhhhhh......hhhhh...............hhhhh.hhhhhhhh................hhh.hhhhhhhhhhhhhhhhhhhh.-----.....hhhh..eeeee.....eeeeehhh...hhhh.eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------TYROSINASE_1      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bt3 A   1 APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLA-----RDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWL 341
                                    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       | -   |   300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                         288   294
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BT3)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPO1_IPOBA | Q9ZP19)
molecular function
    GO:0004097    catechol oxidase activity    Catalysis of the reaction: 2 catechol + O2 = 2 1,2-benzoquinone + 2 H2O.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009543    chloroplast thylakoid lumen    The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPO1_IPOBA | Q9ZP19: 1bt1 1bt2 1bug

(-) Related Entries Specified in the PDB File

1bt1 1bt2 1bug