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(-) Description

Title :  CRYSTAL STRUCTURE OF R275E MUTANT OF BMRR BOUND TO DNA AND RHODAMINE
 
Authors :  K. J. Newberry, R. G. Brennan
Date :  20 May 08  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Multidrug Resistance, Transcription Regulation, Protein-Dna Complex, Activator, Dna-Binding, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Newberry, J. L. Huffman, M. C. Miller, N. Vazquez-Laslop, A. A. Neyfakh, R. G. Brennan
Structures Of Bmrr-Drug Complexes Reveal A Rigid Multidrug Binding Pocket And Transcription Activation Through Tyrosin Expulsion
J. Biol. Chem. V. 283 26795 2008
PubMed-ID: 18658145  |  Reference-DOI: 10.1074/JBC.M804191200

(-) Compounds

Molecule 1 - MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: TOP10
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-278
    Gene: BMRR, BMR1R
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
 
Molecule 2 - BMR PROMOTER DNA
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2RHQ1Ligand/IonRHODAMINE 6G
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2RHQ2Ligand/IonRHODAMINE 6G

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:48 , PRO A:144 , TYR A:152 , TYR A:170 , GLY A:171 , ALA A:172 , ILE A:182 , TYR A:187 , PHE A:224 , GLU A:253 , ILE A:255 , TYR A:268BINDING SITE FOR RESIDUE RHQ A 300
2AC2SOFTWAREDT B:-2 , DT B:1BINDING SITE FOR RESIDUE GOL B 200
3AC3SOFTWAREDT B:1BINDING SITE FOR RESIDUE GOL B 201
4AC4SOFTWAREASP A:54 , SER A:58 , TYR A:84 , PHE A:165 , THR A:166 , ASN A:167 , ASN A:168BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D6Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D6Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D6Z)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MERR_2PS50937 MerR-type HTH domain profile.BMRR_BACSU5-75  1A:5-75
2HTH_MERR_1PS00552 MerR-type HTH domain signature.BMRR_BACSU9-31  1A:9-31
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MERR_2PS50937 MerR-type HTH domain profile.BMRR_BACSU5-75  2A:5-75
2HTH_MERR_1PS00552 MerR-type HTH domain signature.BMRR_BACSU9-31  2A:9-31

(-) Exons   (0, 0)

(no "Exon" information available for 3D6Z)

(-) 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:277
 aligned with BMRR_BACSU | P39075 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       
           BMRR_BACSU     2 KESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIAE 278
               SCOP domains d3d6za1 A:2-120 automated matches                                                                                      d3d6za2 A:121-278 automated matches                                                                                                                            SCOP domains
               CATH domains 3d6zA01 A:2-75  [code=1.10.1660.10, no name defined]                      3d6zA02 A:76-119 Single helix bin           3d6zA03 A:120-278 Multidrug-efflux Transporter 1 Regulator Bmrr; Chain                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhh.hhhhhhhhhhh......ee......eee.hhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeeeee.........hhhhhhhhhhhhhhhhh.....eeeee......hhhhh...eeeee..............eeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HTH_MERR_2  PDB: A:5-75 UniProt: 5-75                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------HTH_MERR_1  PDB: A:9-31------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d6z A   2 KESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIEILD 278
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       


Chain B from PDB  Type:DNA  Length:24
                                                        
                 3d6z B -13 TGACCCTCCCCTTAGGGGAGGGTC  12
                                    -4 ||      8    
                                      -2|           
                                        1
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D6Z)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (BMRR_BACSU | P39075)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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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  BMRR_BACSU | P39075
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 Related Entries

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

UniProtKB/Swiss-Prot
        BMRR_BACSU | P39075: 1bow 1exi 1exj 1r8e 2bow 3d6y 3d70 3d71 3iao 3q1m 3q2y 3q3d 3q5p 3q5r 3q5s

(-) Related Entries Specified in the PDB File

1bow C-TERMINAL FRAGMENT OF BMRR
1exj WTBMRR BOUND TO DNA AND TPP
1r8e WTBMRR BOUND TO DNA AT 2.4 RESOLUTION
2bow C-TERMINAL FRAGMENT OF BMRR BOUND TO TPP
3d6y R275E BMRR BOUND TO DNA AND BERBERINE
3d70 E253A BMRR BOUND TO DNA
3d71