1JTX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REGULATOR QACR BOUND TO CRYSTAL VIOLET

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

Date :   22 Aug 01 (Deposition) - 07 Dec 01 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Multidrug Binding, Repressor, S. Aureus, Qaca, Qacr, Multidrug Recognition, 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	:	PSK
	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 (2, 25)

No.	Name	Count	Type	Full Name
1	CVI	1	Ligand/Ion	CRYSTAL VIOLET
2	SO4	24	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	CVI	1	Ligand/Ion	CRYSTAL VIOLET
2	SO4	13	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 11)

No.	Name	Count	Type	Full Name
1	CVI	-1	Ligand/Ion	CRYSTAL VIOLET
2	SO4	11	Ligand/Ion	SULFATE ION

Asymmetric Unit (25, 25)

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:3 , ASN B:38 , TYR B:41 , LYS B:44	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:24 , GLY D:26	BINDING SITE FOR RESIDUE SO4 D 899
05	AC5	SOFTWARE	THR E:24 , THR E:25 , GLY E:26 , LYS E:36 , SO4 E:249	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 , HOH D:903	BINDING SITE FOR RESIDUE SO4 D 901
08	AC8	SOFTWARE	LYS E:36 , TYR E:40 , LYS E:46 , GLU E:47 , SO4 E:900	BINDING SITE FOR RESIDUE SO4 E 249
09	AC9	SOFTWARE	VAL A:29 , SER A:35 , LYS A:36 , GLY A:37	BINDING SITE FOR RESIDUE SO4 A 699
10	BC1	SOFTWARE	HIS B:128 , LYS B:132	BINDING SITE FOR RESIDUE SO4 B 219
11	BC2	SOFTWARE	LYS E:12 , ILE E:53 , ILE E:56 , GLU E:57	BINDING SITE FOR RESIDUE SO4 E 399
12	BC3	SOFTWARE	LYS A:36 , TYR A:40 , ASN E:2 , ASP E:5	BINDING SITE FOR RESIDUE SO4 A 799
13	BC4	SOFTWARE	TYR A:20 , LYS A:46 , GLU A:47 , GLU A:105 , TYR A:106	BINDING SITE FOR RESIDUE SO4 A 800
14	BC5	SOFTWARE	LYS E:4 , HIS E:42	BINDING SITE FOR RESIDUE SO4 E 901
15	BC6	SOFTWARE	GLN B:64 , TYR B:91 , GLN D:64 , GLU D:90 , TYR D:91	BINDING SITE FOR RESIDUE SO4 B 199
16	BC7	SOFTWARE	LYS B:67 , LYS D:60 , GLU D:90 , TYR D:91 , HOH D:903	BINDING SITE FOR RESIDUE SO4 B 499
17	BC8	SOFTWARE	THR B:45 , LYS B:46 , GLU B:47 , TYR B:106 , SO4 B:999	BINDING SITE FOR RESIDUE SO4 B 700
18	BC9	SOFTWARE	THR B:24 , THR B:25 , LYS B:46 , SO4 B:700	BINDING SITE FOR RESIDUE SO4 B 999
19	CC1	SOFTWARE	HIS A:128 , LYS A:132	BINDING SITE FOR RESIDUE SO4 A 801
20	CC2	SOFTWARE	ASN A:2 , LEU A:3 , LYS A:4 , HIS A:42	BINDING SITE FOR RESIDUE SO4 A 802
21	CC3	SOFTWARE	HIS D:128 , LYS D:132	BINDING SITE FOR RESIDUE SO4 D 902
22	CC4	SOFTWARE	HIS E:128 , LYS E:132 , HOH E:912	BINDING SITE FOR RESIDUE SO4 E 239
23	CC5	SOFTWARE	LYS D:17 , LYS D:30	BINDING SITE FOR RESIDUE SO4 D 779
24	CC6	SOFTWARE	THR E:109 , ASN E:110 , SER E:111	BINDING SITE FOR RESIDUE SO4 E 649
25	CC7	SOFTWARE	THR A:89 , GLU A:90 , TYR A:93 , TYR A:103 , GLU A:120 , TYR A:123 , ILE A:124 , ASN A:154 , ASN A:157 , THR A:161 , ILE B:100	BINDING SITE FOR RESIDUE CVI A 200

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

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

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

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 1JTX)

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 d1jtxa1 A:2-72 Multidrug binding protein QacR                          d1jtxa2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jtxA01 A:2-50 Homeodomain-like                  1jtxA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jtx 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 d1jtxb1 B:2-72 Multidrug binding protein QacR                          d1jtxb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jtxB01 B:2-50 Homeodomain-like                  1jtxB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jtx 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 d1jtxd1 D:2-72 Multidrug binding protein QacR                          d1jtxd2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jtxD01 D:2-50 Homeodomain-like                  1jtxD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jtx 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 d1jtxe1 E:2-72 Multidrug binding protein QacR                          d1jtxe2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 1jtxE01 E:2-50 Homeodomain-like                  1jtxE02 E:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
           Pfam domains (1) -----TetR_N-1jtxE01 E:7-53                          ---TetR_C_5-1jtxE05 E:57-187                                                                                                           Pfam domains (1)
           Pfam domains (2) -----TetR_N-1jtxE02 E:7-53                          ---TetR_C_5-1jtxE06 E:57-187                                                                                                           Pfam domains (2)
           Pfam domains (3) -----TetR_N-1jtxE03 E:7-53                          ---TetR_C_5-1jtxE07 E:57-187                                                                                                           Pfam domains (3)
           Pfam domains (4) -----TetR_N-1jtxE04 E:7-53                          ---TetR_C_5-1jtxE08 E:57-187                                                                                                           Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: E:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jtx 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. (6)

1a	1jtxA01	A:2-50
1b	1jtxB01	B:2-50
1c	1jtxD01	D:2-50
1d	1jtxE01	E:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. (6)

2a	1jtxA02	A:51-187
2b	1jtxB02	B:51-187
2c	1jtxD02	D:51-187
2d	1jtxE02	E:51-187

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Staphylococcus aureus (11)

1a	TetR_N-1jtxE01	E:7-53
1b	TetR_N-1jtxE02	E:7-53
1c	TetR_N-1jtxE03	E:7-53
1d	TetR_N-1jtxE04	E:7-53

Clan: TetR_C (33)

Family: TetR_C_5 (11)

Staphylococcus aureus (11)

2a	TetR_C_5-1jtxE05	E:57-187
2b	TetR_C_5-1jtxE06	E:57-187
2c	TetR_C_5-1jtxE07	E:57-187
2d	TetR_C_5-1jtxE08	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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	1jtx
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	QACR_STAAU \| P0A0N4
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UniProtKB/Swiss-Prot
	QACR_STAAU \| P0A0N4	:	1jt0 1jt6 1jty 1jum 1jup 1jus 1qvt 1qvu 1rkw 1rpw 2dtz 2gby 2hq5

1jt0	QACR-DNA COMPLEX
1jt6	QACR-DEQUALINIUM COMPLEX
1jty	QACR-ETHIDIUM COMPLEX
1jum	QACR-BERBERINE COMPLEX
1jup	QACR-MALCHITE GREEN COMPLEX
1jus	QACR-RHODAMINE 6G COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 25)

Sites (25, 25)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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SCOP Domains (2, 8)

CATH Domains (2, 8)

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