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(-) Description

Title :  STRUCTURE OF THE CORE BINDING DOMAIN OF SIGMA54
 
Authors :  E. Hong, D. Wemmer
Date :  19 Oct 08  (Deposition) - 26 May 09  (Release) - 30 Jun 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Hong, M. Doucleff, D. E. Wemmer
Structure Of The Rna Polymerase Core-Binding Domain Of Sigma(54) Reveals A Likely Conformational Fracture Point
J. Mol. Biol. V. 390 70 2009
PubMed-ID: 19426742  |  Reference-DOI: 10.1016/J.JMB.2009.04.070
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA POLYMERASE SIGMA FACTOR RPON
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET21B3-2
    Fragment: SEQUENCE DATABASE RESIDUES 60-135
    Gene: RPON
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2K9L)

(-) Sites  (0, 0)

(no "Site" information available for 2K9L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K9L)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ile A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K9L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2K9L)

(-) Exons   (0, 0)

(no "Exon" information available for 2K9L)

(-) 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:76
 aligned with O66858_AQUAE | O66858 from UniProtKB/TrEMBL  Length:398

    Alignment length:76
                                    69        79        89        99       109       119       129      
         O66858_AQUAE    60 KETVPYQIPYTPSELEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISDVLRCSVEELEKVRQKVLRLE 135
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2k9l A  60 KETVPYQIPYTPSELEELQQNIKLELEGKEQELALELLNYLNEKGFLSKSVEEISDVLRCSVEELEKVRQKVLRLE 135
                                    69        79        89        99       109       119       129
   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 2K9L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K9L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2K9L)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (O66858_AQUAE | O66858)
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:0016987    sigma factor activity    A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
    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:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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  Cis Peptide Bonds
    Ile A:67 - Pro A:68   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        O66858_AQUAE | O66858: 2ahq 2k9m 2o8k 2o9l 5ui5

(-) Related Entries Specified in the PDB File

2k9m