3BTC - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF QACR(E57Q) BOUND TO MALACHITE GREEN

Authors :   M. A. Schumacher, J. T. Schuman, R. G. Brennan

Date :   28 Dec 07 (Deposition) - 12 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,D,E
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: D,E  (1x)
Biol. Unit 3: A (4x),B (4x),D (4x),E (4x)

Keywords :   Qacr, Multidrug Binding, Malachite Green, Dye, Dna-Binding, Plasmid, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Peters, J. T. Schuman, R. A. Skurray, M. H. Brown, R. G. Brennan, M. A. Schumacher
Qacr-Cation Recognition Is Mediated By A Redundancy Of Residues Capable Of Charge Neutralization
Biochemistry V. 47 8122 2008
PubMed-ID: 18616285 | Reference-DOI: 10.1021/BI8008246
(for further references see the PDB file header)

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR QACR
	Atcc	:	700699
	Chains	:	B, D, A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	QACR
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Strain	:	MU50

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	MGR	1	Ligand/Ion	MALACHITE GREEN
2	SO4	16	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MGR	1	Ligand/Ion	MALACHITE GREEN
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	MGR	-1	Ligand/Ion	MALACHITE GREEN
2	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MGR	-1	Ligand/Ion	MALACHITE GREEN
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:2 , LYS A:6	BINDING SITE FOR RESIDUE SO4 A 599
02	AC2	SOFTWARE	LYS A:4 , TYR A:41 , HIS A:42	BINDING SITE FOR RESIDUE SO4 A 299
03	AC3	SOFTWARE	THR D:25 , TYR D:40 , LYS D:46	BINDING SITE FOR RESIDUE SO4 D 899
04	AC4	SOFTWARE	LYS E:36 , TYR E:40 , THR E:45 , LYS E:46	BINDING SITE FOR RESIDUE SO4 E 900
05	AC5	SOFTWARE	LYS B:66 , LEU D:3 , ASN D:38 , HIS D:42	BINDING SITE FOR RESIDUE SO4 D 269
06	AC6	SOFTWARE	THR D:24 , GLY D:26	BINDING SITE FOR RESIDUE SO4 D 270
07	AC7	SOFTWARE	TYR E:20 , THR E:45 , LYS E:46 , GLU E:47 , TYR E:106	BINDING SITE FOR RESIDUE SO4 E 249
08	AC8	SOFTWARE	ASN A:2 , LEU A:3 , LYS A:4 , ASN A:38 , HIS A:42	BINDING SITE FOR RESIDUE SO4 A 279
09	AC9	SOFTWARE	LYS B:67 , LYS D:60 , TYR D:91	BINDING SITE FOR RESIDUE SO4 B 499
10	BC1	SOFTWARE	LYS E:12 , ILE E:53 , ILE E:56 , GLN E:57 , LYS E:60	BINDING SITE FOR RESIDUE SO4 E 399
11	BC2	SOFTWARE	ASN E:2 , ASP E:5 , LYS E:6	BINDING SITE FOR RESIDUE SO4 E 799
12	BC3	SOFTWARE	LYS A:36 , LYS E:60	BINDING SITE FOR RESIDUE SO4 A 699
13	BC4	SOFTWARE	LYS B:60 , TYR B:91 , LYS D:67	BINDING SITE FOR RESIDUE SO4 B 600
14	BC5	SOFTWARE	HIS A:128 , LYS A:132	BINDING SITE FOR RESIDUE SO4 A 801
15	BC6	SOFTWARE	HIS D:164 , GLU D:165 , TYR E:107	BINDING SITE FOR RESIDUE SO4 D 280
16	BC7	SOFTWARE	HIS E:128 , LYS E:132	BINDING SITE FOR RESIDUE SO4 E 239
17	BC8	SOFTWARE	TYR A:103 , GLU A:120 , TYR A:123 , ILE A:124 , ALA A:153 , ASN A:154 , ASN A:157	BINDING SITE FOR RESIDUE MGR A 200

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

(no "Cis Peptide Bond" information available for 3BTC)

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	QACR_STAAM	19-49	4	A:19-49 B:19-49 D:19-49 E:19-49

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	QACR_STAAM	19-49	2	A:19-49 B:19-49 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	QACR_STAAM	19-49	2	- - D:19-49 E:19-49

Biological Unit 3 (1, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	QACR_STAAM	19-49	16	A:19-49 B:19-49 D:19-49 E:19-49

(no "Exon" information available for 3BTC)

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:186
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           QACR_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btca1 A:2-72 Multidrug binding protein QacR                          d3btca2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btcA01 A:2-50 Homeodomain-like                  3btcA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btc A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIQESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           QACR_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btcb1 B:2-72 Multidrug binding protein QacR                          d3btcb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btcB01 B:2-50 Homeodomain-like                  3btcB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btc B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIQESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain D from PDB  Type:PROTEIN  Length:186
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           QACR_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btcd1 D:2-72 Multidrug binding protein QacR                          d3btcd2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btcD01 D:2-50 Homeodomain-like                  3btcD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btc D   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIQESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain E from PDB  Type:PROTEIN  Length:186
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           QACR_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btce1 E:2-72 Multidrug binding protein QacR                          d3btce2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btcE01 E:2-50 Homeodomain-like                  3btcE02 E:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: E:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btc E   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIQESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

Staphylococcus aureus. Strain: mu50. (5)

1a	3btcA01	A:2-50
1b	3btcD01	D:2-50
1c	3btcE01	E:2-50
1d	3btcB01	B:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Strain: mu50. (5)

2a	3btcA02	A:51-187
2b	3btcB02	B:51-187
2c	3btcD02	D:51-187
2d	3btcE02	E:51-187

(no "Pfam Domain" information available for 3BTC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,E (QACR_STAAM | P0A0N3)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3btc)

Biological Units
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	3btc
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	QACR_STAAM \| P0A0N3
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UniProtKB/Swiss-Prot
	QACR_STAAM \| P0A0N3	:	3bqz 3br0 3br1 3br2 3br3 3br5 3br6 3bt9 3bti 3btj 3btl 3pm1

1jt6	WT QACR BOUND TO DEQUALINIUM
1jty	WT QACR BOUND TO ETHIDIUM
1jum	WT QACR BOUND TO BERBERINE
1jup	WT QACR BOUND TO MALACHITE GREEN
1jus	WT QACR BOUND TO R6G
1qvt	WT QACR BOUND TO PROFLAVINE
3bt9
3bti
3btj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 8)

CATH Domains (2, 8)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File