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(-) Description

Title :  STRUCTURE OF QACR E90Q BOUND TO ETHIDIUM
 
Authors :  M. A. Schumacher
Date :  15 Nov 10  (Deposition) - 13 Jul 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tetr Family Member, Transcription Regulation, Multidrug Resistance, Dna, Nucleoid, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Peters, B. E. Brooks, M. A. Schumacher, R. A. Skurray, R. G. Brennan, M. H. Brown
A Single Acidic Residue Can Guide Binding Site Selection Bu Does Not Govern Qacr Cationic-Drug Affinity.
Plos One V. 6 E1597 2011
PubMed-ID: 21264225  |  Reference-DOI: 10.1371/JOURNAL.PONE.0015974

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR QACR
    Atcc: 700699
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: DH5[ALPHA]
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Gene: QACR
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ET1Ligand/IonETHIDIUM
2SO47Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:76 , TYR B:80 , GLN B:180BINDING SITE FOR RESIDUE SO4 B 500
2AC2SOFTWARELEU B:186 , SER B:187 , HOH B:511BINDING SITE FOR RESIDUE SO4 B 501
3AC3SOFTWARELYS A:177 , ILE B:142 , ASN B:143 , ASP B:144BINDING SITE FOR RESIDUE SO4 B 502
4AC4SOFTWAREHIS B:128 , LYS B:132BINDING SITE FOR RESIDUE SO4 B 507
5AC5SOFTWARETRP A:61 , SER A:86 , GLN A:90 , GLN A:96 , GLU A:120 , TYR A:123 , ASN A:154 , ASN A:157 , HOH A:512BINDING SITE FOR RESIDUE ET A 205
6AC6SOFTWARELYS A:30 , GLU A:33 , GLN B:90 , TYR B:91BINDING SITE FOR RESIDUE SO4 A 503
7AC7SOFTWAREHIS A:128 , LYS A:132BINDING SITE FOR RESIDUE SO4 A 504
8AC8SOFTWARETRP A:140 , SER A:141BINDING SITE FOR RESIDUE SO4 A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PM1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PM1)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.QACR_STAAM1-61  1B:1-61
2HTH_TETR_1PS01081 TetR-type HTH domain signature.QACR_STAAM19-49
 		  2A:19-49
B:19-49

(-) Exons   (0, 0)

(no "Exon" information available for 3PM1)

(-) Sequences/Alignments

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:185
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:185
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     
           QACR_STAAM     3 LKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3pm1a1 A:3-72 Multidrug binding protein QacR                         d3pm1a2 A:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_TETR_2  PDB: - UniProt: 1-61                           ------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ----------------HTH_TETR_1  PDB: A:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pm1 A   3 LKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKSEQIKAKTNREKFYLYNELSLTTQYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with QACR_STAAM | P0A0N3 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
           QACR_STAAM     1 MNLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWCINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLS 187
               SCOP domains d3pm1b1 B:1-72 Multidrug binding protein QacR                           d3pm1b2 B:73-187 Multidrug binding protein QacR                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh-..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_TETR_2  PDB: B:1-61 UniProt: 1-61                        ------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------HTH_TETR_1  PDB: B:19-49       ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pm1 B   1 MNLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKSEQIKAKTNREKFYLYNELSLTTQYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFT-EQNINERIKLMNKFSQIFLNGLS 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  | |  170       180       
                                                                                                                                                                                            163 |                      
                                                                                                                                                                                              165
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  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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PM1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  3pm1
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  QACR_STAAM | P0A0N3
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 Related Entries

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

UniProtKB/Swiss-Prot
        QACR_STAAM | P0A0N3: 3bqz 3br0 3br1 3br2 3br3 3br5 3br6 3bt9 3btc 3bti 3btj 3btl

(-) Related Entries Specified in the PDB File

1jt6 WILDTYPE QACR WITH DEQUALINIUM
1jty WILDTYPE QACR WITH ETHIDIUM
1jup WILDTYPE QACR WITH MALACHITE GREEN
1jus WILDTYPE QACR WITH RHODAMINE 6 G
3bqz MALACHITE GREEN BOUND TO QACR(E90Q)
3br0 MALACHITE GREEN BOUND TO QACR(E120Q)
3br1 DEQUALINIUM BOUND TO QACR(E90Q)
3br2 DEQUALINIUM BOUND TO QACR(E120Q)
3br4 ETHIDIUM BOUND TO QACR(E1200Q)
3br5 RHODAMINE 6G BOUND TO QACR(E90Q)
3br6 RHODAMINE 6G BOUND TO QACR(E120Q)