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(-) Description

Title :  A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF RNA POLYMERASE AND DNA
 
Authors :  B. Dangi, A. M. Gronenborn, J. L. Rosner, R. G. Martin
Date :  18 Oct 04  (Deposition) - 26 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D
Keywords :  Protein-Dna Complex, Ternary Complex, Mara, Rna Polymerase, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Dangi, A. M. Gronenborn, J. L. Rosner, R. G. Martin
Versatility Of The Carboxy-Terminal Domain Of The Alpha Subunit Of Rna Polymerase In Transcriptional Activation: Use Of The Dna Contact Site As A Protein Contact Site For Mara.
Mol. Microbiol. V. 54 45 2004
PubMed-ID: 15458404  |  Reference-DOI: 10.1111/J.1365-2958.2004.04250.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMARA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - 5'- D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*A P*T)-3'
    ChainsB
    EngineeredYES
    FragmentPROMOTER REGION
    SyntheticYES
 
Molecule 3 - 5'- D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*T P*C)-3'
    ChainsC
    EngineeredYES
    FragmentPROMOTER REGION
    SyntheticYES
 
Molecule 4 - DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN
    ChainsD
    EC Number2.7.7.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRPOA, PEZ, PHS, SEZ
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymRNAP ALPHA SUBUNIT, TRANSCRIPTASE ALPHA CHAIN, RNA POLYMERASE ALPHA SUBUNIT

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1XS9)

(-) Sites  (0, 0)

(no "Site" information available for 1XS9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XS9)

(-) PROSITE Motifs  (2, 2)

NMR Structure (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 1XS9)

(-) Sequences/Alignments

NMR Structure
   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:129
 aligned with MARA_ECOLI | P0ACH5 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:129
                              1                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118         
           MARA_ECOLI     - --MSRRNTDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPLNHYNS 127
               SCOP domains d1xs9a_ A: Ternary complex formed between MarA, the alpha-CTD of RNA polymerase and DNA                                           SCOP domains
               CATH domains --------1xs9A01 A:9-64 Homeodomain-like                         1xs9A02 A:65-124 Homeodomain-like                           ----- CATH domains
               Pfam domains --------------------------------HTH_18-1xs9A01 A:33-112                                                         ----------------- Pfam domains
         Sec.struct. author ......hhhhhh...hhhhhhh..........hhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhh....hhhhhhhh................. 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
                 1xs9 A   1 MTMSRRNTDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPLNHYNS 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain B from PDB  Type:DNA  Length:20
                                                    
                 1xs9 B 404 GATTTAGCAAAACGTGGCAT 423
                                   413       423

Chain C from PDB  Type:DNA  Length:20
                                                    
                 1xs9 C 428 ATGCCACGTTTTGCTAAATC 447
                                   437       447

Chain D from PDB  Type:PROTEIN  Length:81
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:81
                                   258       268       278       288       298       308       318       328 
           RPOA_ECOLI   249 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE 329
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xs9D00 D:249-329 5' to 3' exonuclease, C-terminal subdomain                      CATH domains
               Pfam domains RNA_pol_A_CTD-1xs9D01 D:249-309                              -------------------- Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhh.....hhhhhh..hhhhhh.....hhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1xs9 D 249 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE 329
                                   258       268       278       288       298       308       318       328 

   Legend:   → Mismatch (orange background)
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    → 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  (1, 1)

NMR Structure

(-) CATH Domains  (2, 3)

NMR Structure

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (20, 23)

NMR Structure(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.

Chain D   (RPOA_ECOLI | P0A7Z4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MARA_ECOLI | P0ACH51bl0
        RPOA_ECOLI | P0A7Z41bdf 1coo 1lb2 2jzb 3iyd 3k4g 3lu0 3n4m 3n97 4jk1 4jk2 4kmu 4kn4 4kn7 4mex 4mey 4s20 4xsx 4xsy 4xsz 4yg2 4yln 4ylo 4ylp 4zh2 4zh3 4zh4 5byh 5ciz 5ezk 5ipl 5ipm 5ipn 5ms0 5my1 5nsr 5nss 5uac 5uag 5uah 5uaj 5ual 5uaq 5up6 5upc 5vsw 5w1s 5w1t

(-) Related Entries Specified in the PDB File

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