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Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF MALACHITE GREEN BOUND TO QACR(E120Q), A MUTANT OF A MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR

Authors :   B. E. Brooks

Date :   20 Dec 07 (Deposition) - 23 Dec 08 (Release) - 23 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

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

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

Reference :   B. E. Brooks, K. M. Hardie, M. H. Brown, R. A. Skurray, R. G. Brennan
Formal Electrostatic Interactions Do Not Govern Qacr-Cation Affinity
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR QACR
	Atcc	:	700699
	Chains	:	B, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTTQ18
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	QACR
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	MU50

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	IMD	2	Ligand/Ion	IMIDAZOLE
2	MGR	1	Ligand/Ion	MALACHITE GREEN
3	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	IMD	2	Ligand/Ion	IMIDAZOLE
2	MGR	1	Ligand/Ion	MALACHITE GREEN
3	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 30)

No.	Name	Count	Type	Full Name
1	IMD	4	Ligand/Ion	IMIDAZOLE
2	MGR	2	Ligand/Ion	MALACHITE GREEN
3	SO4	24	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG B:76 , TYR B:80 , GLN B:180 , HOH B:540 , HOH B:542 , HOH B:546	BINDING SITE FOR RESIDUE SO4 B 500
02	AC2	SOFTWARE	LYS A:30 , GLU A:33 , HOH A:528 , GLU B:90 , HOH B:524	BINDING SITE FOR RESIDUE SO4 B 501
03	AC3	SOFTWARE	HIS B:128 , LYS B:132	BINDING SITE FOR RESIDUE SO4 B 502
04	AC4	SOFTWARE	LYS A:177 , ILE B:142 , ASN B:143 , ASP B:144	BINDING SITE FOR RESIDUE SO4 B 504
05	AC5	SOFTWARE	THR A:24 , GLY A:26 , LYS A:36 , HOH A:527	BINDING SITE FOR RESIDUE SO4 A 505
06	AC6	SOFTWARE	LYS A:4 , HIS A:42 , HOH A:541	BINDING SITE FOR RESIDUE SO4 A 506
07	AC7	SOFTWARE	ASN A:135 , SER A:141 , ILE A:142	BINDING SITE FOR RESIDUE SO4 A 507
08	AC8	SOFTWARE	HIS A:128 , LYS A:132	BINDING SITE FOR RESIDUE SO4 A 508
09	AC9	SOFTWARE	THR B:24 , GLY B:26 , GLU B:27	BINDING SITE FOR RESIDUE SO4 B 509
10	BC1	SOFTWARE	LYS B:4 , HIS B:42 , HOH B:535	BINDING SITE FOR RESIDUE SO4 B 510
11	BC2	SOFTWARE	LYS A:6 , VAL A:10 , GLU A:13 , TYR A:92	BINDING SITE FOR RESIDUE SO4 A 511
12	BC3	SOFTWARE	ASN B:176 , LYS B:177 , GLN B:180	BINDING SITE FOR RESIDUE SO4 B 512
13	BC4	SOFTWARE	GLU A:90 , TYR A:93 , GLN A:120 , ASN A:154 , ASN A:157 , THR A:161 , IMD A:401 , IMD A:402	BINDING SITE FOR RESIDUE MGR A 200
14	BC5	SOFTWARE	GLU A:58 , TYR A:93 , TYR A:123 , MGR A:200 , IMD A:402	BINDING SITE FOR RESIDUE IMD A 401
15	BC6	SOFTWARE	GLN A:120 , MGR A:200 , IMD A:401	BINDING SITE FOR RESIDUE IMD A 402

(no "SS Bond" information available for 3BR0)

(no "Cis Peptide Bond" information available for 3BR0)

(no "SAP(SNP)/Variant" information available for 3BR0)

Asymmetric Unit (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 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, 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

(no "Exon" information available for 3BR0)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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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 d3br0a1 A:2-72 Multidrug binding protein QacR                          d3br0a2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3br0A01 A:2-50 Homeodomain-like                  3br0A02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3br0 A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKSEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLQNKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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:184
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
           QACR_STAAM     4 KDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3br0b1 B:4-72 Multidrug binding protein QacR                        d3br0b2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3br0B01 B:4-50 Homeodomain-like                3br0B02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3br0 B   4 KDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKSEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLQNKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

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. Organism_taxid: 1280. Strain: mu50. (7)

1a	3br0A01	A:2-50
1b	3br0B01	B:4-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. Strain: mu50. (7)

2a	3br0A02	A:51-187
2b	3br0B02	B:51-187

(no "Pfam Domain" information available for 3BR0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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

1jt6	WILDTYPE QACR WITH DEQUALINIUM
1jty	WILDTYPE QACR WITH ETHIDIUM
1jup	WILDTYPE QACR WITH MALACHITE GREEN
1jus	WILDTYPE QACR WITH RHODAMINE 6 G
3bqz	MALACHITE GREEN BOUND TO QACR(E90Q)
3br1	DEQUALINIUM BOUND TO QACR(E90Q)
3br2	DEQUALINIUM BOUND TO QACR(E120Q)
3br3	ETHIDIUM BOUND TO QACR(E90Q)
3br4	ETHIDIUM BOUND TO QACR(E1200Q)
3br5	RHODAMINE 6G BOUND TO QACR(E90Q)
3br6	RHODAMINE 6G BOUND TO QACR(E120Q)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (5, 5)

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