2GBY - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF QACR MULTIDRUG TRANSCRIPTIONAL REGULATOR BOUND TO BIVALENT DIAMIDINE BERENIL

Authors :   J. T. Schuman

Date :   12 Mar 06 (Deposition) - 08 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,D,E
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: D,E  (1x)
Biol. Unit 3: A (4x),B (4x),D (4x),E (4x)
Biol. Unit 4: A (4x),B (4x),D (4x),E (4x)

Keywords :   Diamidine, Helix-Turn-Helix, Multridrug Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. G. Brennan, J. T. Schuman
Structure Of Qacr Multidrug Transcriptional Regulator Bound To Trivalent And Bivalent Diamidine Drugs
To Be Published
PubMed: search

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR QACR
	Chains	:	B, D, A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	QACR
	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
Biological Unit 3 (4x)	:	A (4x)	B (4x)	D (4x)	E (4x)
Biological Unit 4 (4x)	:	A (4x)	B (4x)	D (4x)	E (4x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	BRN	1	Ligand/Ion	BERENIL
2	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	BRN	1	Ligand/Ion	BERENIL
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	BRN	-1	Ligand/Ion	BERENIL
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	BRN	-1	Ligand/Ion	BERENIL
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 28)

No.	Name	Count	Type	Full Name
1	BRN	4	Ligand/Ion	BERENIL
2	SO4	24	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:100 , TYR A:103 , GLU A:120 , ILE A:124 , ASN A:154 , ASN A:157 , PHE B:162	BINDING SITE FOR RESIDUE BRN A 1110
02	AC2	SOFTWARE	ASN A:2 , ASP A:5 , LYS A:6	BINDING SITE FOR RESIDUE SO4 A 599
03	AC3	SOFTWARE	LYS A:4 , TYR A:41 , HIS A:42 , LYS E:17	BINDING SITE FOR RESIDUE SO4 A 299
04	AC4	SOFTWARE	LYS E:36 , TYR E:40 , THR E:45 , LYS E:46	BINDING SITE FOR RESIDUE SO4 E 249
05	AC5	SOFTWARE	SER A:35 , LYS A:36 , LYS E:60	BINDING SITE FOR RESIDUE SO4 A 699
06	AC6	SOFTWARE	TYR D:20 , LYS D:46 , GLU D:105 , TYR D:106	BINDING SITE FOR RESIDUE SO4 D 999
07	AC7	SOFTWARE	LEU E:8 , LYS E:12 , ILE E:53 , ILE E:56 , GLU E:57	BINDING SITE FOR RESIDUE SO4 E 399
08	AC8	SOFTWARE	LYS A:36 , TYR A:40 , ASN E:2 , ASP E:5 , LYS E:6	BINDING SITE FOR RESIDUE SO4 E 799
09	AC9	SOFTWARE	THR A:23 , THR A:24 , THR A:25 , LYS A:46	BINDING SITE FOR RESIDUE SO4 A 800
10	BC1	SOFTWARE	HIS A:128 , LYS A:132 , HOH A:1112	BINDING SITE FOR RESIDUE SO4 A 801
11	BC2	SOFTWARE	ASN A:2 , LEU A:3 , LYS A:4 , ASN A:38 , HIS A:42	BINDING SITE FOR RESIDUE SO4 A 279
12	BC3	SOFTWARE	GLU D:13 , LYS D:30 , GLU D:33	BINDING SITE FOR RESIDUE SO4 D 779

(no "SS Bond" information available for 2GBY)

(no "Cis Peptide Bond" information available for 2GBY)

(no "SAP(SNP)/Variant" information available for 2GBY)

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

Biological Unit 3 (1, 16)

	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	16	A:19-49 B:19-49 D:19-49 E:19-49

Biological Unit 4 (1, 16)

	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	16	A:19-49 B:19-49 D:19-49 E:19-49

(no "Exon" information available for 2GBY)

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 d2gbya1 A:2-72 Multidrug binding protein QacR                          d2gbya2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 2gbyA01 A:2-50 Homeodomain-like                  2gbyA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gby 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 d2gbyb1 B:2-72 Multidrug binding protein QacR                          d2gbyb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 2gbyB01 B:2-50 Homeodomain-like                  2gbyB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gby 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 d2gbyd1 D:2-72 Multidrug binding protein QacR                          d2gbyd2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 2gbyD01 D:2-50 Homeodomain-like                  2gbyD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gby 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 d2gbye1 E:2-72 Multidrug binding protein QacR                          d2gbye2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 2gbyE01 E:2-50 Homeodomain-like                  2gbyE02 E:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: E:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gby 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	2gbyA01	A:2-50
1b	2gbyB01	B:2-50
1c	2gbyD01	D:2-50
1d	2gbyE01	E:2-50

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Staphylococcus aureus. Organism_taxid: 1280. (7)

2a	2gbyA02	A:51-187
2b	2gbyB02	B:51-187
2c	2gbyD02	D:51-187
2d	2gbyE02	E:51-187

(no "Pfam Domain" information available for 2GBY)

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.

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

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