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(-) Description

Title :  CRYSTAL STRUCTURE OF BMRR BOUND TO KANAMYCIN
 
Authors :  S. Bachas, C Eginton, G Gunio, H Wade
Date :  29 Dec 10  (Deposition) - 20 Jul 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Multidrug Binding, Multidrug Resistance, Transcription Regulator, Transcription-Rna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bachas, C. Eginton, D. Gunio, H. Wade
Structural Contributions To Multidrug Recognition In The Multidrug Resistance (Mdr) Gene Regulator, Bmrr.
Proc. Natl. Acad. Sci. Usa V. 108 11046 2011
PubMed-ID: 21690368  |  Reference-DOI: 10.1073/PNAS.1104850108

(-) Compounds

Molecule 1 - MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BMRR, BMR1R, BSU24020
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - 23 BP PROMOTER DNA
    Chains: B
    Engineered: YES
    Other Details: 23 BP OF THE BMR EFFLUX GENE SYNTHESIZED BY IDT
    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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1KAN1Ligand/IonKANAMYCIN A
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1KAN2Ligand/IonKANAMYCIN A

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:144 , VAL A:147 , ASN A:149 , TYR A:187 , PHE A:224 , TYR A:229 , GLU A:253 , ILE A:255BINDING SITE FOR RESIDUE KAN A 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q5R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q5R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q5R)

(-) 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 3Q5R)

(-) 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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhh.hhhhhhhhhhh......ee......eeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhh.....eeeee......hhhhh.eeeeeee..............eeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhh......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
                 3q5r A   3 ESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGLGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIL 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
                                                       
                 3q5r B -12 GACCCTCCCCTTAGGGGAGGGTC  12
                                    -3||       9   
                                     -2|           
                                       1
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 3Q5R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q5R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q5R)

(-) 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 1r8e 2bow 3d6y 3d6z 3d70 3d71 3iao 3q1m 3q2y 3q3d 3q5p 3q5s

(-) Related Entries Specified in the PDB File

3d6y 3d6z