1QVU - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO TWO DRUGS: ETHIDIUM AND PROFLAVINE

Authors :   M. A. Schumacher, M. C. Miller, R. G. Brennan

Date :   28 Aug 03 (Deposition) - 03 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.96

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

Keywords :   Qacr, Multidrug Binding Protein, Transcription, Repressor, Cooperative Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Schumacher, M. C. Miller, R. G. Brennan
Structural Mechanism Of The Simultaneous Binding Of Two Drugs To A Multidrug-Binding Protein
Embo J. V. 23 2923 2004
PubMed-ID: 15257299 | Reference-DOI: 10.1038/SJ.EMBOJ.7600288
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATOR QACR
	Chains	:	B, D, A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	QACR
	Gene	:	QACR OR SAVP031
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280

		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 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ET	1	Ligand/Ion	ETHIDIUM
2	PRL	1	Ligand/Ion	PROFLAVIN

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ET	-1	Ligand/Ion	ETHIDIUM
2	PRL	1	Ligand/Ion	PROFLAVIN

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ET	-1	Ligand/Ion	ETHIDIUM
2	PRL	-1	Ligand/Ion	PROFLAVIN

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	ET	-1	Ligand/Ion	ETHIDIUM
2	PRL	2	Ligand/Ion	PROFLAVIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:96 , ILE A:100 , TYR A:103 , TYR A:107 , GLU A:120 , TYR A:123 , ASN A:157 , ASN B:97 , PHE B:162	BINDING SITE FOR RESIDUE ET A 195
2	AC2	SOFTWARE	GLU A:58 , TRP A:61 , THR A:89 , GLU A:90 , TYR A:103	BINDING SITE FOR RESIDUE PRL A 196

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

(no "Cis Peptide Bond" information available for 1QVU)

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

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_STAAU	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_STAAU	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_STAAU	19-49	2	- - D:19-49 E:19-49

Biological Unit 3 (1, 4)

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

(no "Exon" information available for 1QVU)

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_STAAU | P0A0N4 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_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d1qvua1 A:2-72 Multidrug binding protein QacR                          d1qvua2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1qvuA01 A:2-50 Homeodomain-like                  1qvuA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qvu A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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_STAAU | P0A0N4 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_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d1qvub1 B:2-72 Multidrug binding protein QacR                          d1qvub2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1qvuB01 B:2-50 Homeodomain-like                  1qvuB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qvu B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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_STAAU | P0A0N4 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_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d1qvud1 D:2-72 Multidrug binding protein QacR                          d1qvud2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1qvuD01 D:2-50 Homeodomain-like                  1qvuD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qvu D   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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_STAAU | P0A0N4 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_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d1qvue1 E:2-72 Multidrug binding protein QacR                          d1qvue2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1qvuE01 E:2-50 Homeodomain-like                  1qvuE02 E:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
           Pfam domains (1) -----TetR_N-1qvuE01 E:7-53                          ---TetR_C_5-1qvuE05 E:57-187                                                                                                           Pfam domains (1)
           Pfam domains (2) -----TetR_N-1qvuE02 E:7-53                          ---TetR_C_5-1qvuE06 E:57-187                                                                                                           Pfam domains (2)
           Pfam domains (3) -----TetR_N-1qvuE03 E:7-53                          ---TetR_C_5-1qvuE07 E:57-187                                                                                                           Pfam domains (3)
           Pfam domains (4) -----TetR_N-1qvuE04 E:7-53                          ---TetR_C_5-1qvuE08 E:57-187                                                                                                           Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: E:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qvu E   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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. Organism_taxid: 1280. (8)

1a	1qvuA01	A:2-50
1b	1qvuB01	B:2-50
1c	1qvuD01	D:2-50
1d	1qvuE01	E:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. (7)

2a	1qvuA02	A:51-187
2b	1qvuB02	B:51-187
2c	1qvuD02	D:51-187
2d	1qvuE02	E:51-187

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Staphylococcus aureus (11)

1a	TetR_N-1qvuE01	E:7-53
1b	TetR_N-1qvuE02	E:7-53
1c	TetR_N-1qvuE03	E:7-53
1d	TetR_N-1qvuE04	E:7-53

Clan: TetR_C (33)

Family: TetR_C_5 (11)

Staphylococcus aureus (11)

2a	TetR_C_5-1qvuE05	E:57-187
2b	TetR_C_5-1qvuE06	E:57-187
2c	TetR_C_5-1qvuE07	E:57-187
2d	TetR_C_5-1qvuE08	E:57-187

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,E (QACR_STAAU | P0A0N4)

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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	1qvu
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	QACR_STAAU \| P0A0N4
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	QACR_STAAU \| P0A0N4
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UniProtKB/Swiss-Prot
	QACR_STAAU \| P0A0N4	:	1jt0 1jt6 1jtx 1jty 1jum 1jup 1jus 1qvt 1rkw 1rpw 2dtz 2gby 2hq5

1jt0	QACR-DNA COMPLEX
1jt6	QACR-DEQUALINIUM COMPLEX
1jtx	QACR-CRYSTAL VIOLET COMPLEX
1jty	QACR-ETHIDIUM COMPLEX
1jus	QACR-R6G COMPLEX
1qvt	QACR-PROFLAVINE COMPLEX

Description

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Ligands, Modified Residues, Ions (2, 2)

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