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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RFAH TRANSCRIPTION FACTOR AT 2.1A RESOLUTION
 
Authors :  D. G. Vassylyev, M. N. Vassylyeva, V. Svetlov, I. Artsimovitch
Date :  10 Feb 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transcription Factor, Virulence, Transcription Pausing, Transcription Elongation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. A. Belogurov, M. N. Vassylyeva, V. Svetlov, S. Klyuyev, N. V. Grishin, D. G. Vassylyev, I. Artsimovitch
Structural Basis For Converting A General Transcription Factor Into An Operon-Specific Virulence Regulator.
Mol. Cell V. 26 117 2007
PubMed-ID: 17434131  |  Reference-DOI: 10.1016/J.MOLCEL.2007.02.021
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL ACTIVATOR RFAH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVS12
    Expression System Strain: BL21 (LAMBDADE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RFAH, HLYT, SFRB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2OUG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OUG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OUG)

(-) Sequences/Alignments

Asymmetric 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:141
 aligned with RFAH_ECOLI | P0AFW0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           RFAH_ECOLI     2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh..eee..eeeeeee....eeeeeee....eeeeee.....hhhhhhhh..eeee...........hhhhhhhhhh.--------------..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oug A   2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYK--------------KVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
                                    11        21        31        41        51        61        71        81        91        |-         -   |   121       131       141       151     
                                                                                                                            100            115                                         


Chain B from PDB  Type:PROTEIN  Length:141
 aligned with RFAH_ECOLI | P0AFW0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           RFAH_ECOLI     2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh..eee..eeeeeee....eeeeeee....eeeeee.....hhhhhhhh..eeee...........hhhhhhhhhh.--------------...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oug B   2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYK--------------KVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
                                    11        21        31        41        51        61        71        81        91        |-         -   |   121       131       141       151     
                                                                                                                            100            115                                         


Chain C from PDB  Type:PROTEIN  Length:141
 aligned with RFAH_ECOLI | P0AFW0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           RFAH_ECOLI     2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh..eee..eeeeeee....eeeeeee....eeeeee.....hhhhhhhh..eeee...........hhhhhhhhhh.--------------...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oug C   2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYK--------------KVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
                                    11        21        31        41        51        61        71        81        91        |-         -   |   121       131       141       151     
                                                                                                                            100            115                                         


Chain D from PDB  Type:PROTEIN  Length:141
 aligned with RFAH_ECOLI | P0AFW0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           RFAH_ECOLI     2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NusG-2ougD01 D:2-91                                                                       ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) NusG-2ougD02 D:2-91                                                                       ----------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) NusG-2ougD03 D:2-91                                                                       ----------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) NusG-2ougD04 D:2-91                                                                       ----------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh..eee..eeeee........eeeee....eeeeee.....hhhhhhhh..eeee...........hhhhhhhhhh.--------------...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oug D   2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYK--------------KVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKN 156
                                    11        21        31        41        51        61        71        81        91        |-         -   |   121       131       141       151     
                                                                                                                            100            115
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (0, 0)

(no "SCOP Domain" information available for 2OUG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NusG-like (8)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RFAH_ECOLI | P0AFW0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001000    bacterial-type RNA polymerase core enzyme binding    Interacting selectively and non-covalently with the bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit.
    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:0001073    transcription antitermination factor activity, DNA binding    Binds to DNA, typically within region of the promoter and transcribed region, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind DNA include the lambda Q protein.
    GO:0008494    translation activator activity    Any of a group of soluble proteins functioning in the activation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0045727    positive regulation of translation    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031564    transcription antitermination    Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
    GO:0001124    transcription elongation from bacterial-type RNA polymerase promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  2oug
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