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(-) Description

Title :  CRYSTAL STRUCTURE OF PPO3, A TYROSINASE FROM AGARICUS BISPORUS, IN DEOXY-FORM THAT CONTAINS ADDITIONAL UNKNOWN LECTIN-LIKE SUBUNIT
 
Authors :  W. T. Ismaya, H. J. Rozeboom, A. Weijn, J. J. Mes, F. Fusetti, H. J. Wicher B. W. Dijkstra
Date :  17 Feb 11  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Oxidoreductase, Copper-Containing, Pigmentation, Type-3 Copper Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. T. Ismaya, H. J. Rozeboom, A. Weijn, J. J. Mes, F. Fusetti, H. J. Wichers, B. W. Dijkstra
Crystal Structure Of Agaricus Bisporus Mushroom Tyrosinase: Identity Of The Tetramer Subunits And Interaction With Tropolone.
Biochemistry V. 50 5477 2011
PubMed-ID: 21598903  |  Reference-DOI: 10.1021/BI200395T

(-) Compounds

Molecule 1 - POLYPHENOL OXIDASE
    Chains: A, B
    EC Number: 1.14.18.1
    Fragment: RESIDUES 2-392
    Organism Common: COMMON MUSHROOM
    Organism Scientific: AGARICUS BISPORUS
    Organism Taxid: 5341
    Other Details: THIOETHER BOND BETWEEN HIS85 AND CYS83
    Other Details - Source: COMMERCIAL
    Synonym: TYROSINASE
 
Molecule 2 - LECTIN-LIKE FOLD PROTEIN
    Chains: C, D
    Organism Common: COMMON MUSHROOM
    Organism Scientific: AGARICUS BISPORUS
    Organism Taxid: 5341
    Other Details: ORF 239342 OF A. BISPORUS GENOME CONSORTIUM
    Other Details - Source: COMMERCIAL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2HO6Ligand/IonHOLMIUM ATOM
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2HO-1Ligand/IonHOLMIUM ATOM
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2HO-1Ligand/IonHOLMIUM ATOM
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:61 , CYS A:83 , HIS A:85 , HIS A:94 , HOH A:2094BINDING SITE FOR RESIDUE CU A 400
02AC2SOFTWAREHIS A:259 , HIS A:263 , HIS A:296 , HOH A:2094BINDING SITE FOR RESIDUE CU A 401
03AC3SOFTWAREASP A:312 , ASP A:336 , GLN A:351 , ASP A:353 , HOH A:2146 , HOH A:2147BINDING SITE FOR RESIDUE HO A 402
04AC4SOFTWAREGLU A:335 , ASP A:353 , HOH A:2118 , HOH A:2124BINDING SITE FOR RESIDUE HO A 403
05AC5SOFTWAREGLU A:16 , HOH A:2148 , HOH A:2149 , GLU B:16BINDING SITE FOR RESIDUE HO A 404
06AC6SOFTWAREASP A:357 , GLU A:359BINDING SITE FOR RESIDUE PEG A1393
07AC7SOFTWAREHIS B:61 , CYS B:83 , HIS B:85 , HIS B:94 , HOH B:2105BINDING SITE FOR RESIDUE CU B 400
08AC8SOFTWAREHIS B:259 , HIS B:263 , HIS B:296 , HOH B:2105BINDING SITE FOR RESIDUE CU B 401
09AC9SOFTWAREASP B:312 , ASP B:336 , GLN B:351 , ASP B:353 , HO B:404 , HOH B:2159 , HOH B:2160BINDING SITE FOR RESIDUE HO B 402
10BC1SOFTWAREGLU B:335 , HO B:404BINDING SITE FOR RESIDUE HO B 403
11BC2SOFTWAREGLU B:335 , ASP B:336 , ASP B:353 , HO B:402 , HO B:403BINDING SITE FOR RESIDUE HO B 404
12BC3SOFTWAREGLU B:356 , ASP B:357 , GLU B:359BINDING SITE FOR RESIDUE PEG B1393
13BC4SOFTWARETHR A:237 , TYR C:58 , LYS C:63 , TRP C:72 , PHE C:87BINDING SITE FOR RESIDUE PEG C1151
14BC5SOFTWARETYR B:236 , HIS D:56 , TYR D:58 , LYS D:63 , TRP D:72 , PHE D:87BINDING SITE FOR RESIDUE PGE D1151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y9W)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Leu A:63 -Pro A:64
2His A:182 -Pro A:183
3Asp A:273 -Pro A:274
4Glu A:340 -Pro A:341
5Leu B:63 -Pro B:64
6His B:182 -Pro B:183
7Asp B:273 -Pro B:274
8Glu B:340 -Pro B:341
9Gly C:128 -Pro C:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y9W)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYROSINASE_2PS00498 Tyrosinase and hemocyanins CuB-binding region signature.PPO3_AGABI289-300
 		  2A:289-300
B:289-300
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYROSINASE_2PS00498 Tyrosinase and hemocyanins CuB-binding region signature.PPO3_AGABI289-300
 		  1A:289-300
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYROSINASE_2PS00498 Tyrosinase and hemocyanins CuB-binding region signature.PPO3_AGABI289-300
 		  1-
B:289-300

(-) Exons   (0, 0)

(no "Exon" information available for 2Y9W)

(-) 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:391
 aligned with PPO3_AGABI | C7FF04 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:391
                                    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       281       291       301       311       321       331       341       351       361       371       381       391 
           PPO3_AGABI     2 SDKKSLMPLVGIPGEIKNRLNILDFVKNDKFFTLYVRALQVLQARDQSDYSSFFQLGGIHGLPYTEWAKAQPQLHLYKANYCTHGTVLFPTWHRAYESTWEQTLWEAAGTVAQRFTTSDQAEWIQAAKDLRQPFWDWGYWPNDPDFIGLPDQVIRDKQVEITDYNGTKIEVENPILHYKFHPIEPTFEGDFAQWQTTMRYPDVQKQENIEGMIAGIKAAAPGFREWTFNMLTKNYTWELFSNHGAVVGAHANSLEMVHNTVHFLIGRDPTLDPLVPGHMGSVPHAAFDPIFWMHHCNVDRLLALWQTMNYDVYVSEGMNREATMGLIPGQVLTEDSPLEPFYTKNQDPWQSDDLEDWETLGFSYPDFDPVKGKSKEEKSVYINDWVHKHYG 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee..hhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...................hhhhhh..eeeee.....eeeee................hhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..........hhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......ee............ee....eeeeee.....eeehhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYROSINASE_2-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y9w A   2 SDKKSLMPLVGIPGEIKNRLNILDFVKNDKFFTLYVRALQVLQARDQSDYSSFFQLGGIHGLPYTEWAKAQPQLHLYKANYCTHGTVLFPTWHRAYESTWEQTLWEAAGTVAQRFTTSDQAEWIQAAKDLRQPFWDWGYWPNDPDFIGLPDQVIRDKQVEITDYNGTKIEVENPILHYKFHPIEPTFEGDFAQWQTTMRYPDVQKQENIEGMIAGIKAAAPGFREWTFNMLTKNYTWELFSNHGAVVGAHANSLEMVHNTVHFLIGRDPTLDPLVPGHMGSVPHAAFDPIFWMHHCNVDRLLALWQTMNYDVYVSEGMNREATMGLIPGQVLTEDSPLEPFYTKNQDPWQSDDLEDWETLGFSYPDFDPVKGKSKEEKSVYINDWVHKHYG 392
                                    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       281       291       301       311       321       331       341       351       361       371       381       391 


Chain B from PDB  Type:PROTEIN  Length:391
 aligned with PPO3_AGABI | C7FF04 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:391
                                    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       281       291       301       311       321       331       341       351       361       371       381       391 
           PPO3_AGABI     2 SDKKSLMPLVGIPGEIKNRLNILDFVKNDKFFTLYVRALQVLQARDQSDYSSFFQLGGIHGLPYTEWAKAQPQLHLYKANYCTHGTVLFPTWHRAYESTWEQTLWEAAGTVAQRFTTSDQAEWIQAAKDLRQPFWDWGYWPNDPDFIGLPDQVIRDKQVEITDYNGTKIEVENPILHYKFHPIEPTFEGDFAQWQTTMRYPDVQKQENIEGMIAGIKAAAPGFREWTFNMLTKNYTWELFSNHGAVVGAHANSLEMVHNTVHFLIGRDPTLDPLVPGHMGSVPHAAFDPIFWMHHCNVDRLLALWQTMNYDVYVSEGMNREATMGLIPGQVLTEDSPLEPFYTKNQDPWQSDDLEDWETLGFSYPDFDPVKGKSKEEKSVYINDWVHKHYG 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee..hhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...................hhhhhh..eeeee.....eeeee...............hhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..........hhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......ee............ee....eeeeee.....eee.hhh.hhhhh.eehhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYROSINASE_2-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y9w B   2 SDKKSLMPLVGIPGEIKNRLNILDFVKNDKFFTLYVRALQVLQARDQSDYSSFFQLGGIHGLPYTEWAKAQPQLHLYKANYCTHGTVLFPTWHRAYESTWEQTLWEAAGTVAQRFTTSDQAEWIQAAKDLRQPFWDWGYWPNDPDFIGLPDQVIRDKQVEITDYNGTKIEVENPILHYKFHPIEPTFEGDFAQWQTTMRYPDVQKQENIEGMIAGIKAAAPGFREWTFNMLTKNYTWELFSNHGAVVGAHANSLEMVHNTVHFLIGRDPTLDPLVPGHMGSVPHAAFDPIFWMHHCNVDRLLALWQTMNYDVYVSEGMNREATMGLIPGQVLTEDSPLEPFYTKNQDPWQSDDLEDWETLGFSYPDFDPVKGKSKEEKSVYINDWVHKHYG 392
                                    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       281       291       301       311       321       331       341       351       361       371       381       391 


Chain C from PDB  Type:PROTEIN  Length:136
 aligned with G1K3P4_AGABI | G1K3P4 from UniProtKB/TrEMBL  Length:150

    Alignment length:142
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148  
         G1K3P4_AGABI     9 LDLPGTRILNGANWANNSATENLATNSGTLIIFDQSTPGQDADRWLIHNYLDGYKIFNMGSNNWASVSRGNTVLGVSEFDGQTCKWSIEYSGNGEEFWIRVPREGGGGAVWTIKPASSQGPTTVFLDLLKETDPNQRIKFAV 150
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..eeeee...------..eeeeee..........eeeeee..eeeeee.....eeee.....eeee..........eeee.....eeeee.........eeeeee......eeeeee.....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y9w C   9 LDLPGTRILNGANWANNSAT------SGTLIIFDQSTPGQDADRWLIHNYLDGYKIFNMGSNNWASVSRGNTVLGVSEFDGQTCKWSIEYSGNGEEFWIRVPREGGGGAVWTIKPASSQGPTTVFLDLLKETDPNQRIKFAV 150
                                    18        28      | 38        48        58        68        78        88        98       108       118       128       138       148  
                                              28     35                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:135
 aligned with G1K3P4_AGABI | G1K3P4 from UniProtKB/TrEMBL  Length:150

    Alignment length:141
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149 
         G1K3P4_AGABI    10 DLPGTRILNGANWANNSATENLATNSGTLIIFDQSTPGQDADRWLIHNYLDGYKIFNMGSNNWASVSRGNTVLGVSEFDGQTCKWSIEYSGNGEEFWIRVPREGGGGAVWTIKPASSQGPTTVFLDLLKETDPNQRIKFAV 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeeee...------..eeeeee..........eeeeee..eeeeee.....eeeee...eeeee..........eeee......eeee.........eeeeee......eeeeee.....hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y9w D  10 DLPGTRILNGANWANNSAT------SGTLIIFDQSTPGQDADRWLIHNYLDGYKIFNMGSNNWASVSRGNTVLGVSEFDGQTCKWSIEYSGNGEEFWIRVPREGGGGAVWTIKPASSQGPTTVFLDLLKETDPNQRIKFAV 150
                                    19        |-     |  39        49        59        69        79        89        99       109       119       129       139       149 
                                             28     35
   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  (0, 0)

(no "SCOP Domain" information available for 2Y9W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y9W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y9W)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PPO3_AGABI | C7FF04)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0004503    monophenol monooxygenase activity    Catalysis of the reaction: L-tyrosine + L-DOPA + O2 = L-DOPA + DOPAquinone + H2O.
    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: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.
    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 C,D   (G1K3P4_AGABI | G1K3P4)

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  PPO3_AGABI | C7FF04
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPO3_AGABI | C7FF04: 2y9x
UniProtKB/TrEMBL
        G1K3P4_AGABI | G1K3P4: 2y9x 5eha

(-) Related Entries Specified in the PDB File

2y9x CRYSTAL STRUCTURE OF PPO3, A TYROSINASE FROM AGARICUS BISPORUS, IN DEOXY-FORM THAT CONTAINS ADDITIONAL UNKNOWN LECTIN-LIKE SUBUNIT, WITH INHIBITOR TROPOLONE