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(-) Description

Title :  CRYSTAL STRUCTURE OF TYROSINASE FROM BACILLUS MEGATERIUM IN COMPLEX WITH SDS
 
Authors :  N. Adir, M. Goldfeder, A. Fishman
Date :  10 Jan 12  (Deposition) - 20 Jun 12  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Type 3 Copper Protein, Tyrosinase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goldfeder, M. Egozy, V. Shuster Ben-Yosef, N. Adir, A. Fishman
Changes In Tyrosinase Specificity By Ionic Liquids And Sodium Dodecyl Sulfate.
Appl. Microbiol. Biotechnol. V. 97 1953 2013
PubMed-ID: 22539021  |  Reference-DOI: 10.1007/S00253-012-4050-Z

(-) 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
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2SDS1Ligand/IonDODECYL SULFATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2SDS1Ligand/IonDODECYL SULFATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2SDS1Ligand/IonDODECYL SULFATE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2SDS-1Ligand/IonDODECYL SULFATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , HIS A:60 , HIS A:69BINDING SITE FOR RESIDUE CU A 401
2AC2SOFTWAREARG A:209BINDING SITE FOR RESIDUE SDS A 402
3AC3SOFTWAREHIS B:42 , HIS B:60 , HIS B:69 , HIS B:231BINDING SITE FOR RESIDUE CU B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D87)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric 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 4D87)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D87)

(-) Exons   (0, 0)

(no "Exon" information available for 4D87)

(-) 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:286
 aligned with B2ZB02_BACME | B2ZB02 from UniProtKB/TrEMBL  Length:297

    Alignment length:286
                                    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 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDIE 289
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhh........hhhhhh....................hhhhh........................................hhhhhhhhhhh..............hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhh.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d87 A   4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDIE 289
                                    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: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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...hhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhh..........hhhhhhh..hhhhh............hhhhh..............ee.....eee................hhhhhhhhh................hhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d87 B   4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVYDI 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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4D87)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D87)

(-) Gene Ontology  (4, 4)

Asymmetric 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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  4d87
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  1.14.18.1
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 Related Entries

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

UniProtKB/TrEMBL
        B2ZB02_BACME | B2ZB02: 3nm8 3npy 3nq0 3nq1 3nq5 3ntm 4hd4 4hd6 4hd7 4j6t 4j6u 4j6v 4p6r 4p6s 4p6t 5i38 5i3a 5i3b

(-) Related Entries Specified in the PDB File

3nm8 3npy 3nq0 3nq1 3nq5 3ntm