3NQ1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF TYROSINASE FROM BACILLUS MEGATERIUM IN COMPLEX WITH INHIBITOR KOJIC ACID

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, Kojic Acid, Oxidoreductase-Oxidoreductase Inhibitor Complex (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, 19)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	KOJ	2	Ligand/Ion	5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE
3	ZN	13	Ligand/Ion	ZINC ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:42 , HIS A:60 , HOH A:353 , HOH A:354 , CU A:502	BINDING SITE FOR RESIDUE CU A 501
02	AC2	SOFTWARE	HIS A:204 , HIS A:208 , HIS A:231 , HOH A:354 , CU A:501	BINDING SITE FOR RESIDUE CU A 502
03	AC3	SOFTWARE	HIS A:13 , HOH A:304 , HOH A:306 , HOH A:357	BINDING SITE FOR RESIDUE ZN A 503
04	AC4	SOFTWARE	GLY A:196 , PHE A:197 , GLY A:200 , ASN A:205 , ARG A:209 , HOH A:335 , HOH A:356 , HOH A:373	BINDING SITE FOR RESIDUE KOJ A 1351
05	AC5	SOFTWARE	ASP A:16 , ASP B:16 , ASP B:112	BINDING SITE FOR RESIDUE ZN A 504
06	AC6	SOFTWARE	GLU A:71 , ARG A:75 , HOH A:364 , HOH A:381	BINDING SITE FOR RESIDUE ZN A 505
07	AC7	SOFTWARE	GLU A:95 , HOH A:321	BINDING SITE FOR RESIDUE ZN A 506
08	AC8	SOFTWARE	ASP A:112 , ASP B:16	BINDING SITE FOR RESIDUE ZN A 507
09	AC9	SOFTWARE	ASP A:166 , ASP B:123	BINDING SITE FOR RESIDUE ZN A 508
10	BC1	SOFTWARE	HIS A:245 , HOH A:369	BINDING SITE FOR RESIDUE ZN A 509
11	BC2	SOFTWARE	HIS A:279 , HOH A:359	BINDING SITE FOR RESIDUE ZN A 510
12	BC3	SOFTWARE	HIS B:42 , HIS B:60 , HOH B:407 , CU B:502	BINDING SITE FOR RESIDUE CU B 501
13	BC4	SOFTWARE	HIS B:204 , HIS B:208 , HIS B:231 , HOH B:407 , CU B:501	BINDING SITE FOR RESIDUE CU B 502
14	BC5	SOFTWARE	HIS B:13 , HOH B:363 , HOH B:371	BINDING SITE FOR RESIDUE ZN B 503
15	BC6	SOFTWARE	GLY B:196 , PHE B:197 , GLY B:200 , PRO B:201 , ASN B:205 , ARG B:209	BINDING SITE FOR RESIDUE KOJ B 1351
16	BC7	SOFTWARE	HOH A:363 , HIS B:49	BINDING SITE FOR RESIDUE ZN B 504
17	BC8	SOFTWARE	GLU B:95 , HOH B:364	BINDING SITE FOR RESIDUE ZN B 505
18	BC9	SOFTWARE	THR B:175 , HIS B:245 , HOH B:388	BINDING SITE FOR RESIDUE ZN B 506
19	CC1	SOFTWARE	HIS B:279 , HOH B:383	BINDING SITE FOR RESIDUE ZN B 507

(no "SS Bond" information available for 3NQ1)

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 3NQ1)

(no "PROSITE Motif" information available for 3NQ1)

(no "Exon" information available for 3NQ1)

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:283
 aligned with B2ZB02_BACME | B2ZB02 from UniProtKB/TrEMBL  Length:297

    Alignment length:283
                                    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 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVY 286
               SCOP domains d3nq1a_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh.....................................................hhhhhhhhhh...............hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nq1 A   4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVY 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

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with B2ZB02_BACME | B2ZB02 from UniProtKB/TrEMBL  Length:297

    Alignment length:283
                                    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 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVY 286
               SCOP domains d3nq1b_ B: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------Tyrosinase-3nq1B01 B:32-244                                                                                                                                                                                          ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------Tyrosinase-3nq1B02 B:32-244                                                                                                                                                                                          ------------------------------------------ Pfam domains (2)
         Sec.struct. author ..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhh.....................................................hhhhhhhhhh...............hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nq1 B   4 KYRVRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGKFHTPPGSDRNAAHMSSAFLPWHREYLLRFERDLQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGNGNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKEAPTLPTRDDVLNALKITQYDTPPWDMTSQNSFRNQLEGFINGPQLHNRVHRWVGGQMGVVPTAPNDPVFFLHHANVDRIWAVWQIIHRNQNYQPMKNGPFGQNFRDPMYPWNTTPEDVMNHRKLGYVY 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

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	d3nq1a_	A:
1b	d3nq1b_	B:

(no "CATH Domain" information available for 3NQ1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Di-copper (13)

Family: Tyrosinase (10)

Bacillus megaterium (6)

1a	Tyrosinase-3nq1B01	B:32-244
1b	Tyrosinase-3nq1B02	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
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KOJ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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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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	3nq1
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (19, 19)

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

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

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