1JT0 | PD0249 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A COOPERATIVE QACR-DNA COMPLEX

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

Date :   20 Aug 01 (Deposition) - 08 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Multidrug Binding Protein, Cooperative Dna Binding, Dimer Of Dimers, Transcription/Dna Complex (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 Basis For Cooperative Dna Binding By Two Dimers Of The Multidrug-Binding Protein Qacr.
Embo J. V. 21 1210 2002
PubMed-ID: 11867549 | Reference-DOI: 10.1093/EMBOJ/21.5.1210
(for further references see the PDB file header)

Molecule 1 - QACA OPERATOR
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
	Chains	:	A, B, C, D
	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	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:60 , TYR B:91	BINDING SITE FOR RESIDUE SO4 B 299
2	AC2	SOFTWARE	LYS D:60 , TYR D:91	BINDING SITE FOR RESIDUE SO4 D 899
3	AC3	SOFTWARE	LYS C:60 , TYR C:91	BINDING SITE FOR RESIDUE SO4 C 699
4	AC4	SOFTWARE	LYS A:60 , TYR A:91	BINDING SITE FOR RESIDUE SO4 A 999
5	AC5	SOFTWARE	ASN B:143 , ASP B:144 , HOH B:402 , LYS D:177	BINDING SITE FOR RESIDUE SO4 B 399

(no "SS Bond" information available for 1JT0)

(no "Cis Peptide Bond" information available for 1JT0)

(no "SAP(SNP)/Variant" information available for 1JT0)

Asymmetric/Biological 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

(no "Exon" information available for 1JT0)

Asymmetric/Biological 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:188
 aligned with QACR_STAAU | P0A0N4 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:188
                                                                                                                                                                                                                    188 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      | 
           QACR_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSK-   -
               SCOP domains d1jt0a1 A:2-72 Multidrug binding protein QacR                          d1jt0a2 A:73-189 Multidrug binding protein QacR                                                                       SCOP domains
               CATH domains 1jt0A01 A:2-50 Homeodomain-like                  1jt0A02 A:51-187 Tetracycline Repressor, domain 2                                                                                        -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jt0 A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSKH 189
                                    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:188
 aligned with QACR_STAAU | P0A0N4 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:188
                                                                                                                                                                                                                    188 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      | 
           QACR_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSK-   -
               SCOP domains d1jt0b1 B:2-72 Multidrug binding protein QacR                          d1jt0b2 B:73-189 Multidrug binding protein QacR                                                                       SCOP domains
               CATH domains 1jt0B01 B:2-50 Homeodomain-like                  1jt0B02 B:51-187 Tetracycline Repressor, domain 2                                                                                        -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jt0 B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSKH 189
                                    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:188
 aligned with QACR_STAAU | P0A0N4 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:188
                                                                                                                                                                                                                    188 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      | 
           QACR_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSK-   -
               SCOP domains d1jt0c1 C:2-72 Multidrug binding protein QacR                          d1jt0c2 C:73-189 Multidrug binding protein QacR                                                                       SCOP domains
               CATH domains 1jt0C01 C:2-50 Homeodomain-like                  1jt0C02 C:51-187 Tetracycline Repressor, domain 2                                                                                        -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: C:19-49       -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jt0 C   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSKH 189
                                    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:185
 aligned with QACR_STAAU | P0A0N4 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           QACR_STAAU     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGL 186
               SCOP domains d1jt0d1 D:2-72 Multidrug binding protein QacR                          d1jt0d2 D:73-186 Multidrug binding protein QacR                                                                    SCOP domains
               CATH domains 1jt0D01 D:2-50 Homeodomain-like                  1jt0D02 D:51-186 Tetracycline Repressor, domain 2                                                                                        CATH domains
           Pfam domains (1) -----TetR_N-1jt0D01 D:7-53                          ---TetR_C_5-1jt0D05 D:57-186                                                                                                          Pfam domains (1)
           Pfam domains (2) -----TetR_N-1jt0D02 D:7-53                          ---TetR_C_5-1jt0D06 D:57-186                                                                                                          Pfam domains (2)
           Pfam domains (3) -----TetR_N-1jt0D03 D:7-53                          ---TetR_C_5-1jt0D07 D:57-186                                                                                                          Pfam domains (3)
           Pfam domains (4) -----TetR_N-1jt0D04 D:7-53                          ---TetR_C_5-1jt0D08 D:57-186                                                                                                          Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jt0 D   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGL 186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain E from PDB  Type:DNA  Length:28
                                                            
                 1jt0 E   7 CTTATAGACCGATCGATCGGTCTATAAG  34
                                    16        26

Chain F from PDB  Type:DNA  Length:28
                                                            
                 1jt0 F   7 CTTATAGACCGATCGATCGGTCTATAAG  34
                                    16        26

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/Biological 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)

[unclassified] (65)

1a	1jt0A01	A:2-50
1b	1jt0B01	B:2-50
1c	1jt0C01	C:2-50
1d	1jt0D01	D:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

[unclassified] (2)

2a	1jt0A02	A:51-187
2b	1jt0B02	B:51-187
2c	1jt0C02	C:51-187
2d	1jt0D02	D:51-186

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Staphylococcus aureus (11)

1a	TetR_N-1jt0D01	D:7-53
1b	TetR_N-1jt0D02	D:7-53
1c	TetR_N-1jt0D03	D:7-53
1d	TetR_N-1jt0D04	D:7-53

Clan: TetR_C (33)

Family: TetR_C_5 (11)

Staphylococcus aureus (11)

2a	TetR_C_5-1jt0D05	D:57-186
2b	TetR_C_5-1jt0D06	D:57-186
2c	TetR_C_5-1jt0D07	D:57-186
2d	TetR_C_5-1jt0D08	D:57-186

Asymmetric/Biological 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/Biological Unit
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	1jt0
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	QACR_STAAU \| P0A0N4	:	1jt6 1jtx 1jty 1jum 1jup 1jus 1qvt 1qvu 1rkw 1rpw 2dtz 2gby 2hq5

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 (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (2, 8)

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