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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MET2-FORM OF THE COPPER-BOUND TYROSINASE IN COMPLEX WITH A CADDIE PROTEIN FROM STREPTOMYCES CASTANEOGLOBISPORUS OBTAINED BY SOAKING IN CUPRIC SULFATE SOLUTION FOR 80 HOURS
 
Authors :  Y. Matoba, M. Sugiyama
Date :  21 Apr 08  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tyrosinase, Binary Complex, Type-3 Copper, Dioxygen, Copper Transfer, Oxidoreductase/Metal Transport Complex, Copper, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matoba, H. Yoshitsu, H. -J. Jeon, K. Oda, M. Noda, T. Kumagai, M. Sugiyama
X-Ray Snapshots Of A Hydroxylation Mechanism Of Tyrosinase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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
    Strain: HUT 6202
 
Molecule 2 - CADDIE
    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
    Strain: HUT 6202
    Synonym: CADDIE PROTEIN ORF378

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1CU5Ligand/IonCOPPER (II) ION
2NO36Ligand/IonNITRATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:175 , HIS A:180 , HOH A:678BINDING SITE FOR RESIDUE CU A 301
02AC2SOFTWAREHIS A:38 , HIS A:54 , HIS A:63 , CU A:303 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE CU A 302
03AC3SOFTWAREHIS A:190 , HIS A:194 , HIS A:216 , CU A:302 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE CU A 303
04AC4SOFTWAREHIS A:277 , HOH A:686BINDING SITE FOR RESIDUE CU A 305
05AC5SOFTWAREARG A:132 , VAL A:133 , ASP A:134 , ARG A:140 , GLN A:200 , THR A:203 , VAL A:205 , HOH A:334BINDING SITE FOR RESIDUE NO3 A 309
06AC6SOFTWARETYR A:165 , TRP A:223 , TRP A:226 , GLN A:227 , ALA A:234 , TYR A:235 , LEU A:263 , HOH A:612BINDING SITE FOR RESIDUE NO3 A 310
07AC7SOFTWARETHR A:238 , GLY A:239 , ASP A:246 , LEU A:247 , ASN A:248 , HOH A:484 , HOH A:536 , LYS B:50 , HOH B:431BINDING SITE FOR RESIDUE NO3 A 312
08AC8SOFTWAREARG A:228 , HIS A:265 , THR A:266 , THR A:270 , PHE A:271 , HOH A:627BINDING SITE FOR RESIDUE NO3 A 313
09AC9SOFTWAREGLU B:67 , HIS B:68 , HIS B:82 , HOH B:558BINDING SITE FOR RESIDUE CU B 304
10BC1SOFTWAREHIS B:82 , VAL B:83 , ILE B:92 , SER B:93 , VAL B:94 , HIS B:97BINDING SITE FOR RESIDUE NO3 B 308
11BC2SOFTWAREGLY A:125 , PRO A:128 , HOH A:444 , THR B:103 , ARG B:105 , ALA B:106 , ARG B:109 , HOH B:398 , HOH B:644BINDING SITE FOR RESIDUE NO3 B 311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZMY)

(-) 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 2ZMY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZMY)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZMY)

(-) 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:277
 aligned with Q83WS2_9ACTN | Q83WS2 from UniProtKB/TrEMBL  Length:273

    Alignment length:277
                                                                                                                                                                                                                                                                                                         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 d2zmya_ 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
                 2zmy A   2 TVRKNQATLTADEKRRFVAAVLELKRSGRYDEFVRTHNEFIMSDTDSGERTGHRSPSFLPWHRRFLLDFEQALQSVDSSVTLPYWDWSADRTVRASLWAPDFLGGTGRSTDGRVMDGPFAASTGNWPINVRVDSRTYLRRSLGGSVAELPTRAEVESVLAISAYDLPPYNSASEGFRNHLEGWRGVNLHNRVHVWVGGQMATGVSPNDPVFWLHHAYVDKLWAEWQRRHPDSAYVPTGGTPDVVDLNETMKPWNTVRPADLLDHTAYYTFDALEHHH 278
                                    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:78
 aligned with Q83WS1_9ACTN | Q83WS1 from UniProtKB/TrEMBL  Length:126

    Alignment length:84
                                    49        59        69        79        89        99       109       119    
         Q83WS1_9ACTN    40 AAPESFDEVYKGRRIQGRPAGGGAHHHEHGGGYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLLPF 123
               SCOP domains d2zmyb_ B: Tyrosinas      e cofactor MelC1                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..eeeeeee.------......eeeee..eee.eee.....eee..eeeeee.hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2zmy B  40 AAPESFDEVYKGRRIQGRPA------HEHGGGYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLLPF 123
                                    49        59      | 69        79        89        99       109       119    
                                              59     66
   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 2ZMY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZMY)

(-) 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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  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 1wx4 1wx5 1wxc 2ahk 2ahl 2zmx 2zmz 2zwd 2zwe 2zwf 2zwg 3aws 3awt 3awu 3awv 3aww 3awx 3awy 3awz 3ax0
        Q83WS2_9ACTN | Q83WS2: 1wx2 1wx4 1wx5 1wxc 2ahk 2ahl 2zmx 2zmz 2zwd 2zwe 2zwf 2zwg 3aws 3awt 3awu 3awv 3aww 3awx 3awy 3awz 3ax0

(-) Related Entries Specified in the PDB File

1wx3 CRYSTAL STRUCTURE OF THE MET1-FORM OF THE COPPER-BOUND TYROSINASE IN COMPLEX WITH A CADDIE PROTEIN FROM STREPTOMYCES CASTANEOGLOBISPORUS OBTAINED BY SOAKING IN CUPRIC SULFATE SOLUTION FOR 36 HOURS
2zmx
2zmz
2zn0
2zn1
2zn2
2zn3
2zn4
2zn5
2zn6