3NM8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TYROSINASE FROM BACILLUS MEGATERIUM

Authors :   M. Sendovski, M. Kanteev, N. Adir, A. Fishman

Date :   22 Jun 10 (Deposition) - 17 Nov 10 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tyrosinase, Type3 Copper Proteins, 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)

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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 17)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	CU	4	Ligand/Ion	COPPER (II) ION
3	ZN	7	Ligand/Ion	ZINC ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:42 , HIS A:60 , HOH A:339 , HOH A:340 , HOH A:344 , CU A:502	BINDING SITE FOR RESIDUE CU A 501
02	AC2	SOFTWARE	HIS A:204 , HIS A:208 , HIS A:231 , HOH A:344 , CU A:501	BINDING SITE FOR RESIDUE CU A 502
03	AC3	SOFTWARE	HIS A:13 , ASP A:287 , CL A:506 , CL A:507	BINDING SITE FOR RESIDUE ZN A 503
04	AC4	SOFTWARE	HIS A:279 , HOH A:329 , HOH A:332 , HOH A:333	BINDING SITE FOR RESIDUE ZN A 504
05	AC5	SOFTWARE	HIS A:245	BINDING SITE FOR RESIDUE ZN A 505
06	AC6	SOFTWARE	LYS A:9 , HIS A:13 , ASP A:287 , ZN A:503 , CL A:507	BINDING SITE FOR RESIDUE CL A 506
07	AC7	SOFTWARE	HIS A:13 , ASP A:287 , ILE A:288 , ZN A:503 , CL A:506 , GLN B:101	BINDING SITE FOR RESIDUE CL A 507
08	AC8	SOFTWARE	HIS B:42 , HIS B:60 , HOH B:307 , HOH B:308 , HOH B:454 , CU B:502	BINDING SITE FOR RESIDUE CU B 501
09	AC9	SOFTWARE	HIS B:204 , HIS B:208 , HIS B:231 , HOH B:307 , CU B:501	BINDING SITE FOR RESIDUE CU B 502
10	BC1	SOFTWARE	HIS B:13 , ASP B:287 , CL B:507 , CL B:508	BINDING SITE FOR RESIDUE ZN B 503
11	BC2	SOFTWARE	HIS B:279 , HOH B:330 , CL B:509 , CL B:510	BINDING SITE FOR RESIDUE ZN B 504
12	BC3	SOFTWARE	HIS A:49	BINDING SITE FOR RESIDUE ZN A 304
13	BC4	SOFTWARE	GLU B:71 , ARG B:75 , THR B:271 , HOH B:309 , HOH B:359	BINDING SITE FOR RESIDUE ZN B 506
14	BC5	SOFTWARE	MET A:100 , GLN A:101 , HOH A:407 , HIS B:13 , ASP B:287 , ILE B:288 , ZN B:503 , CL B:508	BINDING SITE FOR RESIDUE CL B 507
15	BC6	SOFTWARE	LYS B:9 , HIS B:13 , ASP B:287 , ZN B:503 , CL B:507	BINDING SITE FOR RESIDUE CL B 508
16	BC7	SOFTWARE	ALA B:239 , HIS B:279 , HOH B:343 , ZN B:504 , CL B:510	BINDING SITE FOR RESIDUE CL B 509
17	BC8	SOFTWARE	ALA B:239 , ILE B:243 , HIS B:279 , ZN B:504 , CL B:509	BINDING SITE FOR RESIDUE CL B 510

(no "SS Bond" information available for 3NM8)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 3NM8)

(no "PROSITE Motif" information available for 3NM8)

(no "Exon" information available for 3NM8)

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 d3nm8a_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh........hhhhh........................................hhhhhhhhhh...............hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nm8 A   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

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 d3nm8b_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------Tyrosinase-3nm8B01 B:32-244                                                                                                                                                                                          -------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------Tyrosinase-3nm8B02 B:32-244                                                                                                                                                                                          -------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh........hhhhh........................................hhhhhhhhhhh..............hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nm8 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)
		→ 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Di-copper centre-containing domain (47)

Superfamily: Di-copper centre-containing domain (47)

Family: automated matches (12)

Protein domain: automated matches (12)

Bacillus megaterium [TaxId: 1404] (12)

1a	d3nm8a_	A:
1b	d3nm8b_	B:

(no "CATH Domain" information available for 3NM8)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Di-copper (13)

Family: Tyrosinase (10)

Bacillus megaterium (6)

1a	Tyrosinase-3nm8B01	B:32-244
1b	Tyrosinase-3nm8B02	B:32-244

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gln A:251 - Pro A:252	[ RasMol ]
		Gln B:251 - Pro B:252	[ RasMol ]
		Gly A:200 - Pro A:201	[ RasMol ]
		Gly B:200 - Pro B:201	[ RasMol ]
		Pro A:180 - Pro A:181	[ RasMol ]
		Pro B:180 - Pro B:181	[ RasMol ]
		Thr A:50 - Pro A:51	[ RasMol ]
		Thr B:50 - Pro B:51	[ RasMol ]
		Tyr A:267 - Pro A:268	[ RasMol ]
		Tyr B:267 - Pro B:268	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

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