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(-) Description

Title :  MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN (MARA)/DNA COMPLEX
 
Authors :  S. Davies, R. G. Rhee, J. L. Martin, D. R. Rosner
Date :  22 Jul 98  (Deposition) - 02 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transcriptional Activator; A Bipartite Helix-Turn-Helix Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Rhee, R. G. Martin, J. L. Rosner, D. R. Davies
A Novel Dna-Binding Motif In Mara: The First Structure For An Arac Family Transcriptional Activator.
Proc. Natl. Acad. Sci. Usa V. 95 10413 1998
PubMed-ID: 9724717  |  Reference-DOI: 10.1073/PNAS.95.18.10413
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*GP*GP*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP *GP*CP*AP* TP*C)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')
    Chains: C
    Engineered: YES
    Synonym: MARA
    Synthetic: YES
 
Molecule 3 - PROTEIN (MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: N8224
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MARA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: BL21(LAMDADE3)

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1BL0)

(-) Sites  (0, 0)

(no "Site" information available for 1BL0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BL0)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BL0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ARAC_FAMILY_2PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.MARA_ECOLI12-110  1A:14-112
2HTH_ARAC_FAMILY_1PS00041 Bacterial regulatory proteins, araC family signature.MARA_ECOLI62-104  1A:64-106

(-) Exons   (0, 0)

(no "Exon" information available for 1BL0)

(-) 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:116
 aligned with MARA_ECOLI | P0ACH5 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:116
                                    16        26        36        46        56        66        76        86        96       106       116      
           MARA_ECOLI     7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL 122
               SCOP domains d1bl0a1 A:9-62 MarA                                   d1bl0a2 A:63-124 MarA                                          SCOP domains
               CATH domains 1bl0A01 A:9-64 Homeodomain-like                         1bl0A02 A:65-124 Homeodomain-like                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhh.....hhhhhhhhhhhh...hhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----HTH_ARAC_FAMILY_2  PDB: A:14-112 UniProt: 12-110                                                   ------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------HTH_ARAC_FAMILY_1  PDB: A:64-106           ------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1bl0 A   9 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain B from PDB  Type:DNA  Length:24
                                                        
                 1bl0 B 401 GGGGATTTAGCAAAACGTGGCATC 424
                                   410       420    


Chain C from PDB  Type:DNA  Length:24
                                                        
                 1bl0 C 425 CCGATGCCACGTTTTGCTAAATCC 448
                                   434       444
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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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BL0)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MARA_ECOLI | P0ACH5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0019172    glyoxalase III activity    Catalysis of the reaction: methylglyoxal + H2O = D-lactate.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0019243    methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione    The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases 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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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UniProtKB/Swiss-Prot
        MARA_ECOLI | P0ACH5: 1xs9

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