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(-) Description

Title :  CRYSTAL STRUCTURE OF BMRR BOUND TO DNA AT 2.4A RESOLUTION
 
Authors :  K. J. Newberry, R. G. Brennan
Date :  23 Oct 03  (Deposition) - 17 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protein-Dna Complex, Merr-Family Transcription Activator, Multidrug- Binding Protein, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Newberry, R. G. Brennan
The Structural Mechanism For Transcription Activation By Merr Family Member Multidrug Transporter Activation, N Terminus.
J. Biol. Chem. V. 279 20356 2004
PubMed-ID: 14985361  |  Reference-DOI: 10.1074/JBC.M400960200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP *GP*GP*GP*TP*C)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - MULTIDRUG-EFFLUX TRANSPORTER REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BMRR
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2IMD11Ligand/IonIMIDAZOLE
3P4P1Ligand/IonTETRAPHENYLPHOSPHONIUM
Biological Unit 1 (3, 34)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2IMD22Ligand/IonIMIDAZOLE
3P4P2Ligand/IonTETRAPHENYLPHOSPHONIUM

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:5 , TYR A:35 , TYR A:44 , PHE A:230 , LEU A:231 , GLN A:234 , LYS A:235 , LYS A:238 , IMD A:312BINDING SITE FOR RESIDUE P4P A 400
02AC2SOFTWARETYR A:152 , TYR A:170 , TYR A:187 , GLU A:253 , ILE A:255 , IMD A:307BINDING SITE FOR RESIDUE IMD A 302
03AC3SOFTWAREPRO A:144 , HOH A:477BINDING SITE FOR RESIDUE IMD A 303
04AC4SOFTWAREPRO A:144 , TYR A:187 , PHE A:224 , ILE A:255BINDING SITE FOR RESIDUE IMD A 304
05AC5SOFTWAREGLY A:141 , ASP A:183 , MET A:185 , THR A:186 , HOH A:460BINDING SITE FOR RESIDUE IMD A 305
06AC6SOFTWAREGLU A:138 , GLU A:140 , SER A:151 , LYS A:154BINDING SITE FOR RESIDUE IMD A 306
07AC7SOFTWAREVAL A:147 , LEU A:148 , ASN A:149 , IMD A:302 , HOH A:521BINDING SITE FOR RESIDUE IMD A 307
08AC8SOFTWAREGLU A:78 , LYS A:113 , GLU A:117BINDING SITE FOR RESIDUE IMD A 308
09AC9SOFTWAREASP A:54 , SER A:58 , TYR A:84 , PHE A:165 , THR A:166 , ASN A:168BINDING SITE FOR RESIDUE IMD A 309
10BC1SOFTWAREARG A:133 , THR A:196 , LYS A:198 , ILE A:200BINDING SITE FOR RESIDUE IMD A 310
11BC2SOFTWAREGLN A:177 , GLU A:184BINDING SITE FOR RESIDUE IMD A 311
12BC3SOFTWARETYR A:5 , P4P A:400BINDING SITE FOR RESIDUE IMD A 312
13BC4SOFTWAREPHE A:174 , SER A:175 , THR A:186 , ARG A:188 , PRO A:205 , HOH A:407BINDING SITE FOR RESIDUE GOL A 401
14BC5SOFTWAREPHE A:176 , ILE A:203 , GLU A:208 , ILE A:209 , SER A:249 , ASP A:250BINDING SITE FOR RESIDUE GOL A 402
15BC6SOFTWAREDT B:-2 , DT B:1BINDING SITE FOR RESIDUE GOL B 203
16BC7SOFTWAREGLN A:115 , TYR A:118 , ARG A:269BINDING SITE FOR RESIDUE GOL A 403
17BC8SOFTWAREDG B:10 , DT B:11BINDING SITE FOR RESIDUE GOL B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R8E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R8E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R8E)

(-) 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 1R8E)

(-) 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:275
 aligned with BMRR_BACSU | P39075 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     
           BMRR_BACSU     3 ESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIA 277
               SCOP domains d1r8ea1 A:3-120 Transcription activator BmrR                                                                          d1r8ea2 A:121-277 Multidrug-binding domain of transcription activator BmrR                                                                                    SCOP domains
               CATH domains 1r8eA02 A:3-75  [code=1.10.1660.10, no name defined]                     1r8eA03 A:76-119 Single helix bin           1r8eA01 A:120-277 Multidrug-efflux Transporter 1 Regulator Bmrr; Chain                                                                                         CATH domains
               Pfam domains ----MerR-1r8eA01 A:7-45                    ----------------------------------------------------------------------------GyrI-like-1r8eA02 A:122-277                                                                                                                                  Pfam domains
         Sec.struct. author ..eeehhhhhhhhh.hhhhhhhhhhh......ee......eeee.hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..eeeeeee.........hhhhhhhhhhhhhhhhh.....eeeee......hhhhh...eeeee..............eeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..........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
                 1r8e A   3 ESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIA 277
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     


Chain B from PDB  Type:DNA  Length:23
                                                       
                 1r8e B -12 GACCCTCCCCTTAGGGGAGGGTC  12
                                    -3||       9   
                                     -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  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: SHS2 (26)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        BMRR_BACSU | P39075: 1bow 1exi 1exj 2bow 3d6y 3d6z 3d70 3d71 3iao 3q1m 3q2y 3q3d 3q5p 3q5r 3q5s

(-) Related Entries Specified in the PDB File

1bow C-TERMINAL DOMAIN OF PROTEIN
1exi THE SAME PROTEIN-DNA COMPLEX WITH TPSB INSTEAD OF TPP
1exj THE SAME PROTEIN-DNA COMPLEX TO LOWER RESOLUTION
1r8d RELATED TRANSCRIPTIONAL ACTIVATOR FROM THE MERR FAMILY
2bow C-TERMINAL DOMAIN OF PROTEIN BOUND TO TPP