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(-) Description

Title :  CRYSTAL STRUCTURE OF QACR(E58Q) BOUND TO MALACHITE GREEN
 
Authors :  M. A. Schumacher, J. T. Schuman, R. G. Brennan
Date :  28 Dec 07  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (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)
Keywords :  Qacr, Multidrug Binding, Malachite Green, Dye, Dna-Binding, Plasmid, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. M. Peters, J. T. Schuman, R. A. Skurray, M. H. Brown, R. G. Brennan, M. A. Schumacher
Qacr-Cation Recognition Is Mediated By A Redundancy Of Residues Capable Of Charge Neutralization
Biochemistry V. 47 8122 2008
PubMed-ID: 18616285  |  Reference-DOI: 10.1021/BI8008246
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR QACR
    Atcc700699
    ChainsB, D, A, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    GeneQACR
    MutationYES
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    StrainMU50

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABDE
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  DE
Biological Unit 3 (4x)A (4x)B (4x)D (4x)E (4x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1MGR1Ligand/IonMALACHITE GREEN
2SO416Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MGR1Ligand/IonMALACHITE GREEN
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MGR-1Ligand/IonMALACHITE GREEN
2SO410Ligand/IonSULFATE ION
Biological Unit 3 (1, 40)
No.NameCountTypeFull Name
1MGR-1Ligand/IonMALACHITE GREEN
2SO440Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:4 , HIS A:42BINDING SITE FOR RESIDUE SO4 A 299
02AC2SOFTWARETHR E:24 , THR E:25 , GLY E:26 , LYS E:36BINDING SITE FOR RESIDUE SO4 E 900
03AC3SOFTWARETHR D:24 , GLY D:26 , GLU D:27 , LYS D:36BINDING SITE FOR RESIDUE SO4 D 270
04AC4SOFTWARELYS E:36 , TYR E:40 , THR E:45 , LYS E:46BINDING SITE FOR RESIDUE SO4 E 249
05AC5SOFTWARESER A:35 , LYS A:36 , GLY A:37 , LYS E:60BINDING SITE FOR RESIDUE SO4 A 699
06AC6SOFTWARETYR D:20 , LYS D:46 , GLU D:105 , TYR D:106BINDING SITE FOR RESIDUE SO4 D 999
07AC7SOFTWARELYS E:12 , ILE E:53 , ILE E:56 , GLU E:57BINDING SITE FOR RESIDUE SO4 E 399
08AC8SOFTWARELYS A:36 , TYR A:40 , ASN E:2 , ASP E:5 , LYS E:6BINDING SITE FOR RESIDUE SO4 E 799
09AC9SOFTWAREHIS A:128 , LYS A:132BINDING SITE FOR RESIDUE SO4 A 801
10BC1SOFTWAREASN A:2 , LEU A:3 , LYS A:4 , HIS A:42BINDING SITE FOR RESIDUE SO4 A 279
11BC2SOFTWAREHIS E:128 , LYS E:132BINDING SITE FOR RESIDUE SO4 E 239
12BC3SOFTWAREGLU D:13 , ILE D:16 , LYS D:17 , LYS D:30BINDING SITE FOR RESIDUE SO4 D 779
13BC4SOFTWAREGLU A:57 , TRP A:61 , GLN A:64 , TYR A:93BINDING SITE FOR RESIDUE SO4 A 431
14BC5SOFTWARETHR D:23 , THR D:24 , THR D:25 , LYS D:46BINDING SITE FOR RESIDUE SO4 D 432
15BC6SOFTWAREILE A:16 , LYS A:17 , PRO A:94 , ASN A:97BINDING SITE FOR RESIDUE SO4 A 433
16BC7SOFTWAREILE D:16BINDING SITE FOR RESIDUE SO4 D 434
17BC8SOFTWARETRP A:61 , GLU A:90 , TYR A:103 , GLU A:120 , ILE A:124 , ALA A:153 , ASN A:154 , ASN A:157BINDING SITE FOR RESIDUE MGR A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BTL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BTL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BTL)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.QACR_STAAM19-49
 
 
 
  4A:19-49
B:19-49
D:19-49
E:19-49
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.QACR_STAAM19-49
 
 
 
  2A:19-49
B:19-49
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.QACR_STAAM19-49
 
 
 
  2-
-
D:19-49
E:19-49
Biological Unit 3 (1, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.QACR_STAAM19-49
 
 
 
  16A:19-49
B:19-49
D:19-49
E:19-49

(-) Exons   (0, 0)

(no "Exon" information available for 3BTL)

(-) Sequences/Alignments

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_STAAM | P0A0N3 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_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btla1 A:2-72 Multidrug binding protein QacR                          d3btla2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btlA01 A:2-50 Homeodomain-like                  3btlA02 A:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btl A   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEQSKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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_STAAM | P0A0N3 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_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btlb1 B:2-72 Multidrug binding protein QacR                          d3btlb2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btlB01 B:2-50 Homeodomain-like                  3btlB02 B:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btl B   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEQSKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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_STAAM | P0A0N3 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_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btld1 D:2-72 Multidrug binding protein QacR                          d3btld2 D:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btlD01 D:2-50 Homeodomain-like                  3btlD02 D:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: D:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btl D   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEQSKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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_STAAM | P0A0N3 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_STAAM     2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3btle1 E:2-72 Multidrug binding protein QacR                          d3btle2 E:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains 3btlE01 E:2-50 Homeodomain-like                  3btlE02 E:51-187 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: E:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3btl E   2 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEQSKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BTL)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (QACR_STAAM | P0A0N3)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        QACR_STAAM | P0A0N33bqz 3br0 3br1 3br2 3br3 3br5 3br6 3bt9 3btc 3bti 3btj 3pm1

(-) Related Entries Specified in the PDB File

1jt6 WT QACR BOUND TO DEQUALINIUM
1jup WT QACR BOUND TO MALACHITE GREEN
3bt9 QACR(E57Q) BOUND TO DEQUALINIUM
3btc QACR(E57Q) BOUND TO MALACHITE GREEN
3bti QACR(E58Q) BOUND TO BERBERINE
3btj QACR(E58Q) BOUND TO DEQUALINIUM1