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(-) Description

Title :  HOMOLOGY MODELING OF A SIGMA FACTOR HAVING A HELIX-TURN-HELIX MOTIF
 
Authors :  A. Bagchi, T. C. Ghosh
Date :  20 May 05  (Deposition) - 02 May 06  (Release) - 20 Jun 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Rna Polymerase-Sigma Factor, Helix-Turn-Helix (Hth) Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Bagchi, T. C. Ghosh
Structural Study Of Two Proteins Sige And Orf1 To Predict Their Roles In The Biochemical Oxidation Of Sulfur Anions Via The Global Sulfur Oxidation Operon (Sox).
Comput. Biol. Chem. V. 30 227 2006
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA POLYMERASE SIGMA FACTOR SIGE
    ChainsA
    Organism CommonBACTERIA
    Organism ScientificTHIOBACILLUS NOVELLUS
    StrainDSMZ 506T
    SynonymSIGMA FACTOR BINDING TO PROMOTER DNA

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CS9)

(-) Sites  (0, 0)

(no "Site" information available for 2CS9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CS9)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Glu A:78 -Leu A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:172
 aligned with Q9LA18_STANO | Q9LA18 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q9LA18_STANO     1 MRAAIEAALKQDWRRLFSYALHLTGSREAASDLLQSCVVKALSSRSLPADIVSVRAWIFTILRNAWIDEFRRNRADAELTAEPLAEPIEHYDDRVIAAITVRQALERIEPIHREIIELVDLAGFRYAEVAAILGVPQGTVMSRLSRARLSLLAVISEGNVLPLSTRRRHGEK 172
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh.................hhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cs9 A   1 MRAAIEAALKQDWRRLFSYALHLTGSREAASDLLQSCVVKALSSRSLPADIVSVRAWIFTILRNAWIDEFRRNRADAELTAEPLAEPIEHYDDRVIAAITVRQALERIEPIHREIIELVDLAGFRYAEVAAILGVPQGTVMSRLSRARLSLLAVISEGNVLPLSTRRRHGEK 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  

   Legend:   → Mismatch (orange background)
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  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 2CS9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CS9)

(-) Gene Ontology  (6, 6)

Theoretical Model(hide GO term definitions)
Chain A   (Q9LA18_STANO | Q9LA18)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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    Glu A:78 - Leu A:79   [ RasMol ]  
 

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