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(-) Description

Title :  CRYSTAL STRUCTURE OF TYROSINASE FROM BACILLUS MEGATERIUM R209H MUTANT
 
Authors :  M. Sendovski, M. Kanteev, N. Adir, A. Fishman
Date :  29 Jun 10  (Deposition) - 17 Nov 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tyrosinase, Type3 Copper Proteins, Bacillus Megaterium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sendovski, M. Kanteev, V. Shuster Ben-Yosef, N. Adir, A. Fishman
First Structures Of An Active Bacterial Tyrosinase Reveal Copper Plasticity.
J. Mol. Biol. V. 405 227 2011
PubMed-ID: 21040728  |  Reference-DOI: 10.1016/J.JMB.2010.10.048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINASE
    Chains: A, B
    EC Number: 1.14.18.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2ZN10Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:42 , HIS A:60 , HOH A:380 , CU A:502BINDING SITE FOR RESIDUE CU A 501
02AC2SOFTWAREHIS A:204 , HIS A:208 , PHE A:227 , HIS A:231 , CU A:501BINDING SITE FOR RESIDUE CU A 502
03AC3SOFTWAREHIS A:13 , ASP A:287 , HOH A:324 , HOH A:382BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWAREASP A:16 , HOH A:400 , ASP B:16 , ASP B:112BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWAREHIS A:49 , ASN B:144 , HOH B:396BINDING SITE FOR RESIDUE ZN A 505
06AC6SOFTWAREGLU A:71 , ARG A:78 , HOH A:385 , HOH A:398BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWAREASP A:123 , ASP B:166BINDING SITE FOR RESIDUE ZN A 507
08AC8SOFTWAREILE A:243 , HIS A:279 , ARG A:280 , HOH A:326 , HOH A:329BINDING SITE FOR RESIDUE ZN A 508
09AC9SOFTWAREHIS B:42 , HIS B:60 , HIS B:69 , HOH B:393 , CU B:502BINDING SITE FOR RESIDUE CU B 501
10BC1SOFTWAREHIS B:204 , HIS B:208 , HIS B:231 , CU B:501BINDING SITE FOR RESIDUE CU B 502
11BC2SOFTWAREHIS B:13 , ASP B:287 , HOH B:402 , HOH B:404BINDING SITE FOR RESIDUE ZN B 503
12BC3SOFTWAREGLU B:71 , ARG B:75 , THR B:271 , HOH B:401BINDING SITE FOR RESIDUE ZN B 504
13BC4SOFTWAREGLU B:95 , HOH B:305 , HOH B:310BINDING SITE FOR RESIDUE ZN B 505
14BC5SOFTWAREHIS B:279 , HOH B:332 , HOH B:333BINDING SITE FOR RESIDUE ZN B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NQ5)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Thr A:50 -Pro A:51
2Pro A:180 -Pro A:181
3Gly A:200 -Pro A:201
4Gln A:251 -Pro A:252
5Tyr A:267 -Pro A:268
6Thr B:50 -Pro B:51
7Pro B:180 -Pro B:181
8Gly B:200 -Pro B:201
9Gln B:251 -Pro B:252
10Tyr B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NQ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NQ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3NQ5)

(-) 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:285
 aligned with B2ZB02_BACME | B2ZB02 from UniProtKB/TrEMBL  Length:297

    Alignment length:285
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
         B2ZB02_BACME     4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDI 288
               SCOP domains d3nq5a_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh........hhhhh........................................hhhhhhhhh................hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhheee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nq5 A   4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHHWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDI 288
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with B2ZB02_BACME | B2ZB02 from UniProtKB/TrEMBL  Length:297

    Alignment length:285
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
         B2ZB02_BACME     4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDI 288
               SCOP domains d3nq5b_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------Tyrosinase-3nq5B01 B:32-244                                                                                                                                                                                          -------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------Tyrosinase-3nq5B02 B:32-244                                                                                                                                                                                          -------------------------------------------- Pfam domains (2)
         Sec.struct. author ...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh........hhhhh........................................hhhhhhh..................hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.---......................hhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nq5 B   4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHHWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHR---YQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDI 288
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243  |   |253       263       273       283     
                                                                                                                                                                                                                                                                            246 250
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NQ5)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Di-copper (13)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B2ZB02_BACME | B2ZB02)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        B2ZB02_BACME | B2ZB02: 3nm8 3npy 3nq0 3nq1 3ntm 4d87 4hd4 4hd6 4hd7 4j6t 4j6u 4j6v 4p6r 4p6s 4p6t 5i38 5i3a 5i3b

(-) Related Entries Specified in the PDB File

3nm8 3npy 3nq0 3nq1 3ntm