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Title :   CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO PENTAMADINE

Authors :   D. S. Murray, M. A. Schumacher, R. G. Brennan

Date :   23 Nov 03 (Deposition) - 01 Jun 04 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.62

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

Keywords :   Multidrug Recognition, Pent, Qacr, Multidrug Binding Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. S. Murray, M. A. Schumacher, R. G. Brennan
Crystal Structures Of Qacr-Diamidine Complexes Reveal Additional Multidrug-Binding Modes And A Novel Mechanism Of Drug Charge Neutralization.
J. Biol. Chem. V. 279 14365 2004
PubMed-ID: 14726520 | Reference-DOI: 10.1074/JBC.M313870200
(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 Plasmid	:	PSK5210
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	QACR, SAVP031
	Mutation	:	YES
	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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 23)

No.	Name	Count	Type	Full Name
1	PNT	1	Ligand/Ion	1,5-BIS(4-AMIDINOPHENOXY)PENTANE
2	SO4	22	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	PNT	1	Ligand/Ion	1,5-BIS(4-AMIDINOPHENOXY)PENTANE
2	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	PNT	-1	Ligand/Ion	1,5-BIS(4-AMIDINOPHENOXY)PENTANE
2	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:57 , LYS A:60 , TRP A:61 , GLN A:64 , TYR A:82 , SER A:86 , THR A:89 , GLU A:90 , TYR A:93 , TYR A:127 , ALA A:153 , VAL A:156 , ASN A:157	BINDING SITE FOR RESIDUE PNT A 225
02	AC2	SOFTWARE	LYS A:12 , ILE A:53 , ILE A:56 , GLU A:57 , LYS A:60	BINDING SITE FOR RESIDUE SO4 A 199
03	AC3	SOFTWARE	LEU B:8 , LYS B:12 , ILE B:53 , ILE B:56 , GLU B:57	BINDING SITE FOR RESIDUE SO4 B 299
04	AC4	SOFTWARE	LYS A:4 , HIS A:42 , SO4 A:579 , HOH A:723	BINDING SITE FOR RESIDUE SO4 A 399
05	AC5	SOFTWARE	THR D:25 , TYR D:40 , THR D:45 , LYS D:46 , SO4 D:799	BINDING SITE FOR RESIDUE SO4 D 499
06	AC6	SOFTWARE	THR E:24 , THR E:25 , GLY E:26 , GLU E:27 , LYS E:36	BINDING SITE FOR RESIDUE SO4 E 599
07	AC7	SOFTWARE	LYS B:66 , ASN D:2 , LEU D:3 , LYS D:4 , ASN D:38 , HIS D:42	BINDING SITE FOR RESIDUE SO4 D 219
08	AC8	SOFTWARE	THR D:24 , GLY D:26	BINDING SITE FOR RESIDUE SO4 D 229
09	AC9	SOFTWARE	LYS E:36 , TYR E:40 , THR E:45 , LYS E:46	BINDING SITE FOR RESIDUE SO4 E 239
10	BC1	SOFTWARE	VAL A:29 , SER A:35 , LYS A:36 , LYS E:60	BINDING SITE FOR RESIDUE SO4 A 699
11	BC2	SOFTWARE	TYR D:20 , LYS D:46 , GLU D:105 , TYR D:106 , SO4 D:499	BINDING SITE FOR RESIDUE SO4 D 799
12	BC3	SOFTWARE	LYS E:12 , ILE E:53 , ILE E:56 , GLU E:57	BINDING SITE FOR RESIDUE SO4 E 899
13	BC4	SOFTWARE	LYS A:36 , TYR A:40 , ASN E:2 , ASP E:5 , LYS E:6	BINDING SITE FOR RESIDUE SO4 E 999
14	BC5	SOFTWARE	LYS E:4 , HIS E:42	BINDING SITE FOR RESIDUE SO4 E 249
15	BC6	SOFTWARE	GLN B:64 , TYR B:91 , GLN D:64 , TYR D:91	BINDING SITE FOR RESIDUE SO4 B 259
16	BC7	SOFTWARE	THR B:24 , THR B:25 , LYS B:46	BINDING SITE FOR RESIDUE SO4 B 269
17	BC8	SOFTWARE	ASN A:2 , LEU A:3 , LYS A:4 , ASN A:38 , HIS A:42	BINDING SITE FOR RESIDUE SO4 A 279
18	BC9	SOFTWARE	ILE B:70 , LYS B:73 , HIS D:164 , GLN D:166 , TYR E:107	BINDING SITE FOR RESIDUE SO4 D 289
19	CC1	SOFTWARE	HIS E:128 , LYS E:132	BINDING SITE FOR RESIDUE SO4 E 209
20	CC2	SOFTWARE	LYS D:17 , LYS D:30 , GLU D:33	BINDING SITE FOR RESIDUE SO4 D 779
21	CC3	SOFTWARE	ASN A:2 , TYR D:107	BINDING SITE FOR RESIDUE SO4 D 539
22	CC4	SOFTWARE	LYS D:173 , ASN E:143 , ASP E:144 , ALA E:147	BINDING SITE FOR RESIDUE SO4 D 639
23	CC5	SOFTWARE	LYS A:4 , HIS A:42 , PHE A:43 , GLU A:52 , SO4 A:399	BINDING SITE FOR RESIDUE SO4 A 579

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

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

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

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

(no "Exon" information available for 1RKW)

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
	(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 d1rkwa1 A:2-72 Multidrug binding protein QacR                          d1rkwa2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rkwA01 A:2-50 Homeodomain-like                  1rkwA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rkw A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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 d1rkwb1 B:2-72 Multidrug binding protein QacR                          d1rkwb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rkwB01 B:2-50 Homeodomain-like                  1rkwB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rkw B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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 d1rkwd1 D:2-72 Multidrug binding protein QacR                          d1rkwd2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rkwD01 D:2-50 Homeodomain-like                  1rkwD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rkw D   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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 d1rkwe1 E:2-72 Multidrug binding protein QacR                          d1rkwe2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rkwE01 E:2-50 Homeodomain-like                  1rkwE02 E:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
           Pfam domains (1) -----TetR_N-1rkwE01 E:7-53                          ---TetR_C_5-1rkwE05 E:57-187                                                                                                           Pfam domains (1)
           Pfam domains (2) -----TetR_N-1rkwE02 E:7-53                          ---TetR_C_5-1rkwE06 E:57-187                                                                                                           Pfam domains (2)
           Pfam domains (3) -----TetR_N-1rkwE03 E:7-53                          ---TetR_C_5-1rkwE07 E:57-187                                                                                                           Pfam domains (3)
           Pfam domains (4) -----TetR_N-1rkwE04 E:7-53                          ---TetR_C_5-1rkwE08 E:57-187                                                                                                           Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..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
                 1rkw E   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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	1rkwA01	A:2-50
1b	1rkwB01	B:2-50
1c	1rkwD01	D:2-50
1d	1rkwE01	E:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. (7)

2a	1rkwA02	A:51-187
2b	1rkwB02	B:51-187
2c	1rkwD02	D:51-187
2d	1rkwE02	E:51-187

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Staphylococcus aureus (11)

1a	TetR_N-1rkwE01	E:7-53
1b	TetR_N-1rkwE02	E:7-53
1c	TetR_N-1rkwE03	E:7-53
1d	TetR_N-1rkwE04	E:7-53

Clan: TetR_C (33)

Family: TetR_C_5 (11)

Staphylococcus aureus (11)

2a	TetR_C_5-1rkwE05	E:57-187
2b	TetR_C_5-1rkwE06	E:57-187
2c	TetR_C_5-1rkwE07	E:57-187
2d	TetR_C_5-1rkwE08	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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	Cis Peptide Bonds
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	1rkw
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UniProtKB/Swiss-Prot
	QACR_STAAU \| P0A0N4	:	1jt0 1jt6 1jtx 1jty 1jum 1jup 1jus 1qvt 1qvu 1rpw 2dtz 2gby 2hq5

1jt6	CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING PROTEIN QACR BOUND TO DEQUALINIUM
1jtx	RYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REGULATOR QACR BOUND TO CRYSTAL VIOLET
1jty	CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REGULATOR QACR BOUND TO ETHIDIUM
1jum	CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO THE NATURAL DRUG BERBERINE
1jup	CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO MALACHITE GREEN
1jus	CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO RHODAMINE 6G

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 23)

Sites (23, 23)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (2, 8)

CATH Domains (2, 8)

Pfam Domains (2, 8)

Gene Ontology (5, 5)

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Related Entries Specified in the PDB File