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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXY-FORM OF THE COPPER-BOUND STREPTOMYCES CASTANEOGLOBISPORUS TYROSINASE COMPLEXED WITH A CADDIE PROTEIN PREPARED BY THE ADDITION OF DITHIOTHREITOL
 
Authors :  Y. Matoba, T. Kumagai, A. Yamamoto, H. Yoshitsu, M. Sugiyama
Date :  19 Jan 05  (Deposition) - 31 Jan 06  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tyrosinase, Binary Complex, Type-3 Copper, Dioxygen, Oxidoreductase- Metal Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matoba, T. Kumagai, A. Yamamoto, H. Yoshitsu, M. Sugiyama
Crystallographic Evidence That The Dinuclear Copper Center Of Tyrosinase Is Flexible During Catalysis
J. Biol. Chem. V. 281 8981 2006
PubMed-ID: 16436386  |  Reference-DOI: 10.1074/JBC.M509785200

(-) Compounds

Molecule 1 - TYROSINASE
    Chains: A
    EC Number: 1.14.18.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-MEL2
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TYRC
    Organism Scientific: STREPTOMYCES CASTANEOGLOBISPORUS
    Organism Taxid: 79261
 
Molecule 2 - MELC
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-MEL2
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ORF378
    Organism Scientific: STREPTOMYCES CASTANEOGLOBISPORUS
    Organism Taxid: 79261
    Synonym: CADDIE PROTEIN ORF378

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2NO35Ligand/IonNITRATE ION
3PER1Ligand/IonPEROXIDE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:38 , HIS A:54 , HIS A:63 , CU A:401 , PER A:409BINDING SITE FOR RESIDUE CU A 400
02AC2SOFTWAREHIS A:190 , HIS A:194 , HIS A:216 , CU A:400 , PER A:409BINDING SITE FOR RESIDUE CU A 401
03AC3SOFTWAREHIS B:82BINDING SITE FOR RESIDUE CU B 402
04AC4SOFTWAREHOH A:707BINDING SITE FOR RESIDUE CU A 403
05AC5SOFTWARETYR A:165 , TRP A:223 , TRP A:226 , GLN A:227 , ALA A:234 , TYR A:235 , LEU A:263 , HOH A:564BINDING SITE FOR RESIDUE NO3 A 404
06AC6SOFTWAREGLY A:125 , PRO A:128 , HOH A:666 , THR B:103 , ARG B:105 , ALA B:106 , ARG B:109 , HOH B:489BINDING SITE FOR RESIDUE NO3 B 405
07AC7SOFTWARETHR A:238 , GLY A:239 , ASP A:246 , LEU A:247 , ASN A:248 , HOH A:635 , HOH A:665 , LYS B:50 , HOH B:458BINDING SITE FOR RESIDUE NO3 A 406
08AC8SOFTWAREHIS B:82 , VAL B:83 , MET B:84 , SER B:93 , VAL B:94 , HIS B:97BINDING SITE FOR RESIDUE NO3 B 407
09AC9SOFTWAREARG A:228 , HIS A:265 , THR A:270 , PHE A:271 , LEU A:274BINDING SITE FOR RESIDUE NO3 A 408
10BC1SOFTWAREHIS A:38 , HIS A:54 , HIS A:63 , HIS A:190 , HIS A:194 , PHE A:212 , HIS A:216 , CU A:400 , CU A:401 , TYR B:98BINDING SITE FOR RESIDUE PER A 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WX4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:168 -Pro A:169
2Val A:236 -Pro A:237
3Lys A:252 -Pro A:253

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WX4)

(-) Exons   (0, 0)

(no "Exon" information available for 1WX4)

(-) 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:273
 aligned with Q83WS2_9ACTN | Q83WS2 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                                                                                                                                                                                                                                                                                         273 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271 | 
         Q83WS2_9ACTN     2 TVRKNQATLTADEKRRFVAAVLELKRSGRYDEFVRTHNEFIMSDTDSGERTGHRSPSFLPWHRRFLLDFEQALQSVDSSVTLPYWDWSADRTVRASLWAPDFLGGTGRSTDGRVMDGPFAAFTGNWPINVRVDSRTYLRRSLGGSVAELPTRAEVESVLAISAYDLPPYNSASEGFRNHLEGWRGVNLHNRVHVWVGGQMATGVSPNDPVFWLHHAYVDKLWAEWQRRHPDSAYVPTGGTPDVVDLNETMKPWNTVRPADLLDHTAYYTFDA-   -
               SCOP domains d1wx4a_ A: Tyrosinase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh.................hhhhh....................hhhhh..........................hhhhhhhhhh..............hhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wx4 A   2 TVRKNQATLTADEKRRFVAAVLELKRSGRYDEFVRTHNEFIMSDTDSGERTGHRSPSFLPWHRRFLLDFEQALQSVDSSVTLPYWDWSADRTVRASLWAPDFLGGTGRSTDGRVMDGPFAASTGNWPINVRVDSRTYLRRSLGGSVAELPTRAEVESVLAISAYDLPPYNSASEGFRNHLEGWRGVNLHNRVHVWVGGQMATGVSPNDPVFWLHHAYVDKLWAEWQRRHPDSAYVPTGGTPDVVDLNETMKPWNTVRPADLLDHTAYYTFDAL 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   


Chain B from PDB  Type:PROTEIN  Length:71
 aligned with Q83WS1_9ACTN | Q83WS1 from UniProtKB/TrEMBL  Length:126

    Alignment length:82
                                    49        59        69        79        89        99       109       119  
         Q83WS1_9ACTN    40 AAPESFDEVYKGRRIQGRPAGGGAHHHEHGGGYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLL 121
               SCOP domains d1wx4b_ B: Tyrosinas           e cofactor MelC1                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeee..-----------..eeee..eee.eee.....eee..eeeeee.hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1wx4 B  40 AAPESFDEVYKGRRIQGRPA-----------GYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLL 121
                                    49        59         - |      79        89        99       109       119  
                                              59          71
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WX4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WX4)

(-) Gene Ontology  (6, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q83WS2_9ACTN | Q83WS2)
molecular function
    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.

Chain B   (Q83WS1_9ACTN | Q83WS1)
molecular function
    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.
biological process
    GO:0042438    melanin biosynthetic process    The chemical reactions and pathways resulting in the formation of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.

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  1wx4
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  Q83WS1_9ACTN | Q83WS1
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  Q83WS2_9ACTN | Q83WS2
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 Related Entries

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

UniProtKB/TrEMBL
        Q83WS1_9ACTN | Q83WS1: 1wx2 1wx5 1wxc 2ahk 2ahl 2zmx 2zmy 2zmz 2zwd 2zwe 2zwf 2zwg 3aws 3awt 3awu 3awv 3aww 3awx 3awy 3awz 3ax0
        Q83WS2_9ACTN | Q83WS2: 1wx2 1wx5 1wxc 2ahk 2ahl 2zmx 2zmy 2zmz 2zwd 2zwe 2zwf 2zwg 3aws 3awt 3awu 3awv 3aww 3awx 3awy 3awz 3ax0

(-) Related Entries Specified in the PDB File

1wx2 THE OXY-FORM OF THE COPPER-BOUND SAME PROTEIN PREPARED BY THE ADDITION OF HYDROGENPEROXIDE
1wx3 THE MET-FORM OF THE COPPER-BOUND SAME PROTEIN
1wx5 THE COPPER-FREE SAME PROTEIN IN THE MONOCLINIC CRYSTAL
1wxc THE COPPER-FREE SAME PROTEIN