1JUS - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO RHODAMINE 6G

Authors :   M. A. Schumacher, M. C. Miller, S. Grkovic, M. H. Brown, R. A. Skurray, R. G. Brennan

Date :   27 Aug 01 (Deposition) - 12 Dec 01 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.84

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

Keywords :   Multidrug Recognition, S. Aureus, Qacr, Rhodamine 6G, Cationic Lipophilic Drugs, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Schumacher, M. C. Miller, S. Grkovic, M. H. Brown, R. A. Skurray, R. G. Brennan
Structural Mechanisms Of Qacr Induction And Multidrug Recognition.
Science V. 294 2158 2001
PubMed-ID: 11739955 | Reference-DOI: 10.1126/SCIENCE.1066020
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
	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
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	QACR REPRESSOR, ORF 188

		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 (3, 32)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	RHQ	1	Ligand/Ion	RHODAMINE 6G
3	SO4	23	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	RHQ	1	Ligand/Ion	RHODAMINE 6G
3	SO4	13	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	RHQ	-1	Ligand/Ion	RHODAMINE 6G
3	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:2 , ASP A:5 , LYS A:6	BINDING SITE FOR RESIDUE SO4 A 599
02	AC2	SOFTWARE	LEU B:8 , LYS B:12 , ILE B:53 , ILE B:56 , GLU B:57 , LYS B:60	BINDING SITE FOR RESIDUE SO4 B 600
03	AC3	SOFTWARE	LYS A:4 , HIS A:42	BINDING SITE FOR RESIDUE SO4 A 299
04	AC4	SOFTWARE	THR D:25 , TYR D:40 , THR D:45 , LYS D:46 , HOH D:1009	BINDING SITE FOR RESIDUE SO4 D 899
05	AC5	SOFTWARE	THR E:24 , THR E:25 , GLY E:26 , LYS E:36	BINDING SITE FOR RESIDUE SO4 E 900
06	AC6	SOFTWARE	LYS B:66 , LEU D:3 , LYS D:4 , HIS D:42	BINDING SITE FOR RESIDUE SO4 D 900
07	AC7	SOFTWARE	LEU D:8 , LYS D:12 , ILE D:56 , GLU D:57	BINDING SITE FOR RESIDUE SO4 D 901
08	AC8	SOFTWARE	LYS E:36 , TYR E:40 , LYS E:46 , GLU E:47	BINDING SITE FOR RESIDUE SO4 E 901
09	AC9	SOFTWARE	SER A:35 , LYS A:36 , GLY A:37	BINDING SITE FOR RESIDUE SO4 A 699
10	BC1	SOFTWARE	ASN D:2 , ASP D:5 , LYS D:6	BINDING SITE FOR RESIDUE SO4 D 999
11	BC2	SOFTWARE	HIS B:128 , LYS B:132 , TYR D:41	BINDING SITE FOR RESIDUE SO4 B 601
12	BC3	SOFTWARE	LYS E:12 , ILE E:56 , GLU E:57	BINDING SITE FOR RESIDUE SO4 E 399
13	BC4	SOFTWARE	LYS A:36 , TYR A:40 , ASN E:2 , ASP E:5 , LYS E:6	BINDING SITE FOR RESIDUE SO4 A 799
14	BC5	SOFTWARE	THR A:23 , THR A:24 , THR A:25 , LYS A:46	BINDING SITE FOR RESIDUE SO4 A 800
15	BC6	SOFTWARE	LYS E:4 , TYR E:41 , HIS E:42	BINDING SITE FOR RESIDUE SO4 E 902
16	BC7	SOFTWARE	GLN B:64 , GLU B:90 , TYR B:91 , GLN D:64 , TYR D:91	BINDING SITE FOR RESIDUE SO4 B 199
17	BC8	SOFTWARE	LYS B:67 , LYS D:60 , GLU D:90 , TYR D:91	BINDING SITE FOR RESIDUE SO4 B 499
18	BC9	SOFTWARE	SER B:35 , LYS B:36 , GLY B:37 , ASN B:38 , LYS B:44	BINDING SITE FOR RESIDUE SO4 B 700
19	CC1	SOFTWARE	THR B:24 , THR B:25 , LYS B:46	BINDING SITE FOR RESIDUE SO4 B 1000
20	CC2	SOFTWARE	HIS A:128 , LYS A:132	BINDING SITE FOR RESIDUE SO4 A 801
21	CC3	SOFTWARE	LEU A:3 , LYS A:4 , ASN A:38 , HIS A:42 , GLU E:13	BINDING SITE FOR RESIDUE SO4 A 802
22	CC4	SOFTWARE	LYS B:73 , HOH B:1010 , HIS D:164 , GLU D:165 , GLN D:166 , TYR E:107	BINDING SITE FOR RESIDUE SO4 D 1000
23	CC5	SOFTWARE	HIS E:128 , LYS E:132 , HOH E:915	BINDING SITE FOR RESIDUE SO4 E 903
24	CC6	SOFTWARE	LEU A:54 , GLU A:58 , TRP A:61 , GLN A:64 , THR A:89 , GLU A:90 , TYR A:93 , GLN A:96 , ILE A:99 , TYR A:123 , VAL A:160 , THR A:161 , HOH A:825	BINDING SITE FOR RESIDUE RHQ A 201

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

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

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

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 1JUS)

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 d1jusa1 A:2-72 Multidrug binding protein QacR                          d1jusa2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jusA01 A:2-50 Homeodomain-like                  1jusA02 A:51-185 Tetracycline Repressor, domain 2                                                                                      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jus A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKmNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLmNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111    |  121       131       141       151       161       171   |   181      
                                                                                                                                            116-MSE                                                    175-MSE

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 d1jusb1 B:2-72 Multidrug binding protein QacR                          d1jusb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jusB01 B:2-50 Homeodomain-like                  1jusB02 B:51-185 Tetracycline Repressor, domain 2                                                                                      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jus B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKmNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLmNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111    |  121       131       141       151       161       171   |   181      
                                                                                                                                            116-MSE                                                    175-MSE

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 d1jusd1 D:2-72 Multidrug binding protein QacR                          d1jusd2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains -------------------------1jusD01 D:27-75 Homeodomain-like                 1jusD02 D:76-185 Tetracycline Repressor, domain 2                                                             -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jus D   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKmNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLmNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111    |  121       131       141       151       161       171   |   181      
                                                                                                                                            116-MSE                                                    175-MSE

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 d1juse1 E:2-72 Multidrug binding protein QacR                          d1juse2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jusE01 E:2-50 Homeodomain-like                  1jusE02 E:51-185 Tetracycline Repressor, domain 2                                                                                      -- CATH domains
           Pfam domains (1) -----TetR_N-1jusE01 E:7-53                          ---TetR_C_5-1jusE05 E:57-187                                                                                                           Pfam domains (1)
           Pfam domains (2) -----TetR_N-1jusE02 E:7-53                          ---TetR_C_5-1jusE06 E:57-187                                                                                                           Pfam domains (2)
           Pfam domains (3) -----TetR_N-1jusE03 E:7-53                          ---TetR_C_5-1jusE07 E:57-187                                                                                                           Pfam domains (3)
           Pfam domains (4) -----TetR_N-1jusE04 E:7-53                          ---TetR_C_5-1jusE08 E:57-187                                                                                                           Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: E:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jus E   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKmNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLmNKFSQIFLNGLS 187
                                    11        21        31        41        51        61        71        81        91       101       111    |  121       131       141       151       161       171   |   181      
                                                                                                                                            116-MSE                                                    175-MSE

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. (6)

1a	1jusA01	A:2-50
1b	1jusB01	B:2-50
1c	1jusE01	E:2-50
1d	1jusD01	D:27-75

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. (6)

2a	1jusA02	A:51-185
2b	1jusB02	B:51-185
2c	1jusE02	E:51-185
2d	1jusD02	D:76-185

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Staphylococcus aureus (11)

1a	TetR_N-1jusE01	E:7-53
1b	TetR_N-1jusE02	E:7-53
1c	TetR_N-1jusE03	E:7-53
1d	TetR_N-1jusE04	E:7-53

Clan: TetR_C (33)

Family: TetR_C_5 (11)

Staphylococcus aureus (11)

2a	TetR_C_5-1jusE05	E:57-187
2b	TetR_C_5-1jusE06	E:57-187
2c	TetR_C_5-1jusE07	E:57-187
2d	TetR_C_5-1jusE08	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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	1jus
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	QACR_STAAU \| P0A0N4
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UniProtKB/Swiss-Prot
	QACR_STAAU \| P0A0N4	:	1jt0 1jt6 1jtx 1jty 1jum 1jup 1qvt 1qvu 1rkw 1rpw 2dtz 2gby 2hq5

1jt0	QACR-DNA COMPLEX
1jt6	QACR-DEQUALINIUM COMPLEX
1jtx	QACR-CRYSTAL VIOLET COMPLEX
1jty	QACR-ETHIDIUM COMPLEX
1jum	QACR-BERBERINE COMPLEX
1jup	QACR-MALCHITE GREEN COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 32)

Sites (24, 24)

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

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (2, 8)

Pfam Domains (2, 8)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File