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(-) Description

Title :  TRP RNA-BINDING ATTENUATION PROTEIN: MODIFYING SYMMETRY AND STABILITY OF A CIRCULAR OLIGOMER
 
Authors :  O. W. Bayfield, C. Chen, A. R. Patterson, W. Luan, C. Smits, P. Gollnick, A. A. Antson
Date :  12 Jul 12  (Deposition) - 19 Sep 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Transcription, Transcription Regulation, Thermofluor, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. W. Bayfield, C. Chen, A. R. Patterson, W. Luan, C. Smits, P. Gollnick A. A. Antson
Trp Rna-Binding Attenuation Protein: Modifying Symmetry And Stability Of A Circular Oligomer.
Plos One V. 7 44309 2012
PubMed-ID: 22970197  |  Reference-DOI: 10.1371/JOURNAL.PONE.0044309

(-) Compounds

Molecule 1 - TRANSCRIPTION ATTENUATION PROTEIN MTRB
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET9A
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: TRP RNA-BINDING ATTENUATION PROTEIN, TRP RNA-BINDING ATTENUATION PROTEIN, TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1TRP6Ligand/IonTRYPTOPHAN
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1TRP12Ligand/IonTRYPTOPHAN

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:23 , GLN A:47 , THR A:49 , THR A:52 , THR F:25 , ARG F:26 , GLY F:27 , ASP F:29 , THR F:30 , SER F:53BINDING SITE FOR RESIDUE TRP A 81
2AC2SOFTWARETHR A:25 , ARG A:26 , GLY A:27 , ASP A:29 , THR A:30 , SER A:53 , GLY B:23 , GLN B:47 , THR B:49 , THR B:52BINDING SITE FOR RESIDUE TRP B 81
3AC3SOFTWARETHR B:25 , ARG B:26 , GLY B:27 , ASP B:29 , THR B:30 , SER B:53 , GLY C:23 , GLN C:47 , THR C:49 , THR C:52BINDING SITE FOR RESIDUE TRP C 81
4AC4SOFTWARETHR C:25 , ARG C:26 , GLY C:27 , ASP C:29 , THR C:30 , SER C:53 , GLY D:23 , GLN D:47 , THR D:49 , THR D:52BINDING SITE FOR RESIDUE TRP D 81
5AC5SOFTWARETHR D:25 , ARG D:26 , GLY D:27 , ASP D:29 , THR D:30 , SER D:53 , GLY E:23 , GLN E:47 , THR E:49 , THR E:52BINDING SITE FOR RESIDUE TRP E 81
6AC6SOFTWARETHR E:25 , ARG E:26 , GLY E:27 , ASP E:29 , THR E:30 , SER E:53 , GLY F:23 , GLN F:47 , THR F:49 , THR F:52BINDING SITE FOR RESIDUE TRP F 81

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B27)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B27)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B27)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B27)

(-) Exons   (0, 0)

(no "Exon" information available for 4B27)

(-) 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:64
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:64
                                    16        26        36        46        56        66    
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
               SCOP domains d4b27a_ A: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b27 A  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
                                    16        26        36        46        56        66    


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:64
                                    16        26        36        46        56        66    
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
               SCOP domains d4b27b_ B: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b27 B  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
                                    16        26        36        46        56        66    


Chain C from PDB  Type:PROTEIN  Length:64
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:64
                                    16        26        36        46        56        66    
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
               SCOP domains d4b27c_ C: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b27 C  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
                                    16        26        36        46        56        66    


Chain D from PDB  Type:PROTEIN  Length:64
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:64
                                    16        26        36        46        56        66    
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
               SCOP domains d4b27d_ D: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b27 D  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
                                    16        26        36        46        56        66    


Chain E from PDB  Type:PROTEIN  Length:64
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:64
                                    16        26        36        46        56        66    
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
               SCOP domains d4b27e_ E: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b27 E  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
                                    16        26        36        46        56        66    


Chain F from PDB  Type:PROTEIN  Length:64
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:64
                                    16        26        36        46        56        66    
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
               SCOP domains d4b27f_ F: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b27 F  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEM 70
                                    16        26        36        46        56        66
   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  (1, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B27)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (MTRB_BACSU | P19466)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        MTRB_BACSU | P19466: 1wap 3zzq

(-) Related Entries Specified in the PDB File

1wap TRP RNA-BINDING ATTENUATION PROTEIN IN COMPLEX WITH 1WAP 3L-TRYPTOPHAN 1WAP 4
3zzq ENGINEERED 12-SUBUNIT BACILLUS SUBTILIS TRP RNA-BINDING ATTENUATION PROTEIN (TRAP)