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(-) Description

Title :  SIGMA-28(FLIA)/FLGM COMPLEX
 
Authors :  M. K. Sorenson, S. S. Ray, S. A. Darst
Date :  11 Feb 04  (Deposition) - 06 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Polymerase Sigma Factor, Anti-Sigma Factor, Transcription, Flagellar Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. K. Sorenson, S. S. Ray, S. A. Darst
Crystal Structure Of The Flagellar Sigma/Anti-Sigma Complex Sigma(28)/Flgm Reveals An Intact Sigma Factor In An Inactive Conformation.
Mol. Cell V. 14 127 2004
PubMed-ID: 15068809  |  Reference-DOI: 10.1016/S1097-2765(04)00150-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA POLYMERASE SIGMA FACTOR FLIA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKMS5
    Expression System StrainBL21-RIL-CODON(+)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFLIA
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
 
Molecule 2 - ANTI-SIGMA FACTOR FLGM
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKMS5
    Expression System StrainBL21-RIL-CODON(+)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFLGM
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1SC5)

(-) Sites  (0, 0)

(no "Site" information available for 1SC5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SC5)

(-) Exons   (0, 0)

(no "Exon" information available for 1SC5)

(-) 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:228
 aligned with O67268_AQUAE | O67268 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
         O67268_AQUAE     2 KNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREMLS 233
               SCOP domains d1sc5a3 A:2-86 Sigma factor sigma-28 (FliA)                                          d1sc5a1 A:87-163 Sigma factor sigma-28 (FliA)                                ----d1sc5a2 A:168-233 Sigma factor sigma-28 (FliA)                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------Sigma70_r2-1sc5A01 A:14-86                                               ------Sigma70_r3-1sc5A02 A:93-168                                                 ------------Sigma70_r4-1sc5A03 A:181-230                      --- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....----...hhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sc5 A   2 KNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSST----EVIKRELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREMLS 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 |    |171       181       191       201       211       221       231  
                                                                                                                                                                                           163  168                                                                 

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with O66683_AQUAE | O66683 from UniProtKB/TrEMBL  Length:88

    Alignment length:86
                                    12        22        32        42        52        62        72        82      
         O66683_AQUAE     3 NRIELSRLIGLLLETEKRKNTEQKESGTNKIEDKVTLSKIAQELSKNDVEEKDLEKKVKELKEKIEKGEYEVSDEKVVKGLIEFFT  88
               SCOP domains d1sc5b_ B: Anti              -sigma factor FlgM                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------FlgM-1sc5B01 B:35-87                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.--------------hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1sc5 B   3 NRIELSRLIGLLLET--------------KIEDKVTLSKIAQELSKNDVEEKDLEKKVKELKEKIEKGEYEVSDEKVVKGLIEFFT  88
                                    12    |    -        32        42        52        62        72        82      
                                         17             32                                                        

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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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1SC5)

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O67268_AQUAE | O67268)
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.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain B   (O66683_AQUAE | O66683)
biological process
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        O66683_AQUAE | O666831rp3
        O67268_AQUAE | O672681rp3

(-) Related Entries Specified in the PDB File

1rp3 SIGMA-28(FLIA)/FLGM COMPLEX AT HIGHER RESOLUTION.