1WX5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE COPPER-FREE STREPTOMYCES CASTANEOGLOBISPORUS TYROSINASE COMPLEXED WITH A CADDIE PROTEIN IN THE MONOCLINIC CRYSTAL

Authors :   Y. Matoba, T. Kumagai, A. Yamamoto, H. Yoshitsu, M. Sugiyama

Date :   19 Jan 05 (Deposition) - 31 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Tyrosinase, Binary Complex, Flexibility, 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
(for further references see the PDB file header)

Molecule 1 - TYROSINASE
	Chains	:	A, C
	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, D
	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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR C:241 , VAL C:244 , ASP C:246 , GLU C:249 , HOH C:463	BINDING SITE FOR RESIDUE NA C 282
2	AC2	SOFTWARE	THR A:241 , VAL A:244 , ASP A:246 , GLU A:249 , HOH A:322 , HOH A:423	BINDING SITE FOR RESIDUE NA A 282
3	AC3	SOFTWARE	GLU C:50 , ARG C:51 , THR C:52 , ASP C:243 , VAL C:244	BINDING SITE FOR RESIDUE NA C 283
4	AC4	SOFTWARE	HIS A:265 , THR A:270 , PHE A:271	BINDING SITE FOR RESIDUE CL A 283
5	AC5	SOFTWARE	TRP A:223 , GLN A:227	BINDING SITE FOR RESIDUE CL A 284

(no "SS Bond" information available for 1WX5)

Asymmetric Unit

No.	Residues
1	Pro A:168	-	Pro A:169
2	Val A:236	-	Pro A:237
3	Lys A:252	-	Pro A:253
4	Pro C:168	-	Pro C:169
5	Val C:236	-	Pro C:237
6	Lys C:252	-	Pro C:253

(no "SAP(SNP)/Variant" information available for 1WX5)

(no "PROSITE Motif" information available for 1WX5)

(no "Exon" information available for 1WX5)

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:275
 aligned with Q83WS2_9ACTN | Q83WS2 from UniProtKB/TrEMBL  Length:273

    Alignment length:275
                                                                                                                                                                                                                                                                                                         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 d1wx5a_ A: Tyrosinase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...................hhhhh....................hhhhh..........................hhhhhhhhhh..............hhhhhhhh.....hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhh.hhhhh.ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wx5 A   2 TVRKNQATLTADEKRRFVAAVLELKRSGRYDEFVRTHNEFIMSDTDSGERTGHRSPSFLPWHRRFLLDFEQALQSVDSSVTLPYWDWSADRTVRASLWAPDFLGGTGRSTDGRVMDGPFAASTGNWPINVRVDSRTYLRRSLGGSVAELPTRAEVESVLAISAYDLPPYNSASEGFRNHLEGWRGVNLHNRVHVWVGGQMATGVSPNDPVFWLHHAYVDKLWAEWQRRHPDSAYVPTGGTPDVVDLNETMKPWNTVRPADLLDHTAYYTFDALEH 276
                                    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
                                    50        60        70        80        90       100       110       120  
         Q83WS1_9ACTN    41 APESFDEVYKGRRIQGRPAGGGAHHHEHGGGYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLLP 122
               SCOP domains d1wx5b_ B: Tyrosina           se cofactor MelC1                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeeee..-----------..eeee..ee..eee.....eee..eeeeee.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1wx5 B  41 APESFDEVYKGRRIQGRPA-----------GYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLLP 122
                                    50        |-         -|       80        90       100       110       120  
                                             59          71

Chain C 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 d1wx5c_ C: Tyrosinase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...................hhhhh....................hhhhh..........................hhhhhhhhhh..............hhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wx5 C   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 D from PDB  Type:PROTEIN  Length:75
 aligned with Q83WS1_9ACTN | Q83WS1 from UniProtKB/TrEMBL  Length:126

    Alignment length:82
                                    50        60        70        80        90       100       110       120  
         Q83WS1_9ACTN    41 APESFDEVYKGRRIQGRPAGGGAHHHEHGGGYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLLP 122
               SCOP domains d1wx5d_ D: Tyrosina       se cofactor MelC1                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeeeee.-------.....eeeee..ee..eee.....eee..eeeeee.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1wx5 D  41 APESFDEVYKGRRIQGRPA-------EHGGGYEVFVDGVQLHVMRNADGSWISVVSHYDPVPTPRAAARAAVDELQGAPLLP 122
                                    50        |-      | 70        80        90       100       110       120  
                                             59      67

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 '\|'

(no "CATH Domain" information available for 1WX5)

(no "Pfam Domain" information available for 1WX5)

Asymmetric Unit(hide GO term definitions)

Chain A,C (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,D (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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Lys A:252 - Pro A:253	[ RasMol ]
		Lys C:252 - Pro C:253	[ RasMol ]
		Pro A:168 - Pro A:169	[ RasMol ]
		Pro C:168 - Pro C:169	[ RasMol ]
		Val A:236 - Pro A:237	[ RasMol ]
		Val C:236 - Pro C:237	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1wx5
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	Q83WS1_9ACTN \| Q83WS1
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	Q83WS2_9ACTN \| Q83WS2
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	1.14.18.1
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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
1wx4	THE OXY-FORM OF THE COPPER-BOUND SAME PROTEIN PREPARED BY THE ADDITION OF DITHIOTHREITOL
1wxc	THE COPPER-FREE SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File