1RPW - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING PROTEIN QACR BOUND TO THE DIAMIDINE HEXAMIDINE

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

Date :   03 Dec 03 (Deposition) - 01 Jun 04 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Qacr Hexamidine, 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	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Gene	:	QACR, SAVP031
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 21)

No.	Name	Count	Type	Full Name
1	DID	1	Ligand/Ion	4,4'[1,6-HEXANEDIYLBIS(OXY)]BISBENZENECARBOXIMIDAMIDE
2	SO4	20	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	DID	1	Ligand/Ion	4,4'[1,6-HEXANEDIYLBIS(OXY)]BISBENZENECARBOXIMIDAMIDE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	DID	-1	Ligand/Ion	4,4'[1,6-HEXANEDIYLBIS(OXY)]BISBENZENECARBOXIMIDAMIDE
2	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS B:4 , HIS B:42	BINDING SITE FOR RESIDUE SO4 B 189
02	AC2	SOFTWARE	THR C:25 , TYR C:40 , THR C:45 , LYS C:46 , SO4 C:192	BINDING SITE FOR RESIDUE SO4 C 189
03	AC3	SOFTWARE	THR D:24 , GLY D:26 , GLU D:27 , LYS D:36	BINDING SITE FOR RESIDUE SO4 D 189
04	AC4	SOFTWARE	LYS A:66 , ASN C:2 , LEU C:3 , LYS C:4 , ASN C:38 , HIS C:42	BINDING SITE FOR RESIDUE SO4 C 190
05	AC5	SOFTWARE	THR C:24 , GLY C:26	BINDING SITE FOR RESIDUE SO4 C 191
06	AC6	SOFTWARE	LYS D:36 , TYR D:40 , THR D:45 , LYS D:46	BINDING SITE FOR RESIDUE SO4 D 190
07	AC7	SOFTWARE	SER B:35 , LYS B:36 , LYS D:60	BINDING SITE FOR RESIDUE SO4 B 190
08	AC8	SOFTWARE	TYR C:20 , LYS C:46 , GLU C:105 , TYR C:106 , SO4 C:189	BINDING SITE FOR RESIDUE SO4 C 192
09	AC9	SOFTWARE	LYS D:12 , ILE D:53 , ILE D:56 , GLU D:57	BINDING SITE FOR RESIDUE SO4 D 191
10	BC1	SOFTWARE	LYS B:36 , TYR B:40 , ASN D:2 , ASP D:5 , LYS D:6	BINDING SITE FOR RESIDUE SO4 D 192
11	BC2	SOFTWARE	GLN A:64 , TYR A:91 , GLN C:64 , GLU C:90 , TYR C:91	BINDING SITE FOR RESIDUE SO4 A 189
12	BC3	SOFTWARE	THR A:24 , THR A:25 , LYS A:46	BINDING SITE FOR RESIDUE SO4 A 190
13	BC4	SOFTWARE	HIS D:128 , LYS D:132	BINDING SITE FOR RESIDUE SO4 D 193
14	BC5	SOFTWARE	GLU C:13 , LYS C:17 , LYS C:30	BINDING SITE FOR RESIDUE SO4 C 193
15	BC6	SOFTWARE	ASN B:2 , LEU B:3 , LYS B:4 , ASN B:38 , HIS B:42	BINDING SITE FOR RESIDUE SO4 B 191
16	BC7	SOFTWARE	LYS A:73 , HIS C:164 , GLU C:165 , GLN C:166	BINDING SITE FOR RESIDUE SO4 C 194
17	BC8	SOFTWARE	TYR C:107 , HIS D:164	BINDING SITE FOR RESIDUE SO4 D 194
18	BC9	SOFTWARE	ASP B:144 , ASN B:146 , ALA B:147	BINDING SITE FOR RESIDUE SO4 B 192
19	CC1	SOFTWARE	ASN D:135 , SER D:141 , ILE D:142	BINDING SITE FOR RESIDUE SO4 D 195
20	CC2	SOFTWARE	SER D:187	BINDING SITE FOR RESIDUE SO4 D 196
21	CC3	SOFTWARE	PHE A:162 , GLU B:57 , TRP B:61 , GLN B:64 , TYR B:93 , GLU B:120 , ILE B:124 , ASN B:154 , ASN B:157 , HOH B:199 , HOH B:200	BINDING SITE FOR RESIDUE DID B 193

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

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

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

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 C:19-49 D: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	- - C:19-49 D:19-49

(no "Exon" information available for 1RPW)

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 d1rpwa1 A:2-72 Multidrug binding protein QacR                          d1rpwa2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rpwA01 A:2-50 Homeodomain-like                  1rpwA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rpw 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 d1rpwb1 B:2-72 Multidrug binding protein QacR                          d1rpwb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rpwB01 B:2-50 Homeodomain-like                  1rpwB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rpw B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain C 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 d1rpwc1 C:2-72 Multidrug binding protein QacR                          d1rpwc2 C:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rpwC01 C:2-50 Homeodomain-like                  1rpwC02 C:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: C:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rpw C   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 d1rpwd1 D:2-72 Multidrug binding protein QacR                          d1rpwd2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1rpwD01 D:2-50 Homeodomain-like                  1rpwD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
           Pfam domains (1) -----TetR_N-1rpwD01 D:7-53                          ---TetR_C_5-1rpwD05 D:57-187                                                                                                           Pfam domains (1)
           Pfam domains (2) -----TetR_N-1rpwD02 D:7-53                          ---TetR_C_5-1rpwD06 D:57-187                                                                                                           Pfam domains (2)
           Pfam domains (3) -----TetR_N-1rpwD03 D:7-53                          ---TetR_C_5-1rpwD07 D:57-187                                                                                                           Pfam domains (3)
           Pfam domains (4) -----TetR_N-1rpwD04 D:7-53                          ---TetR_C_5-1rpwD08 D:57-187                                                                                                           Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rpw D   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	1rpwA01	A:2-50
1b	1rpwB01	B:2-50
1c	1rpwC01	C:2-50
1d	1rpwD01	D:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. (7)

2a	1rpwA02	A:51-187
2b	1rpwB02	B:51-187
2c	1rpwC02	C:51-187
2d	1rpwD02	D:51-187

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Staphylococcus aureus (11)

1a	TetR_N-1rpwD01	D:7-53
1b	TetR_N-1rpwD02	D:7-53
1c	TetR_N-1rpwD03	D:7-53
1d	TetR_N-1rpwD04	D:7-53

Clan: TetR_C (33)

Family: TetR_C_5 (11)

Staphylococcus aureus (11)

2a	TetR_C_5-1rpwD05	D:57-187
2b	TetR_C_5-1rpwD06	D:57-187
2c	TetR_C_5-1rpwD07	D:57-187
2d	TetR_C_5-1rpwD08	D:57-187

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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	1rpw
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	QACR_STAAU \| P0A0N4
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	QACR_STAAU \| P0A0N4	:	1jt0 1jt6 1jtx 1jty 1jum 1jup 1jus 1qvt 1qvu 1rkw 2dtz 2gby 2hq5

1jt6	QACR BOUND TO DEQUALINIUM
1jty	QACR BOUND TO ETHIDIUM
1jus	QACR BOUND TO RHODAMINE 6G

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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SCOP Domains (2, 8)

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