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(-) Description

Title :  ENGINEERED 12-SUBUNIT BACILLUS SUBTILIS TRP RNA-BINDING ATTENUATION PROTEIN (TRAP)
 
Authors :  C. Chen, C. Smits, G. G. Dodson, M. B. Shevtsov, N. Merlino, P. Gollnick, A. A. Antson
Date :  02 Sep 11  (Deposition) - 12 Oct 11  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Transcription, Transcription Regulation, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chen, C. Smits, G. G. Dodson, M. B. Shevtsov, N. Merlino, P. Gollnick A. A. Antson
How To Change The Oligomeric State Of A Circular Protein Assembly: Switch From 11-Subunit To 12-Subunit Trap Suggests A General Mechanism
Plos One V. 6 25296 2011
PubMed-ID: 21984911  |  Reference-DOI: 10.1371/JOURNAL.PONE.0025296

(-) Compounds

Molecule 1 - TRANSCRIPTION ATTENUATION PROTEIN MTRB
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET9A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 7-71
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Other Details: THE LAST FOUR RESIDUES ARE REMOVED IN B.SUBTILIS TRAP. K71STOP CODON
    Synonym: TRP RNA-BINDING ATTENUATION PROTEIN, TRAP, 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, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1TRP12Ligand/IonTRYPTOPHAN
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1TRP24Ligand/IonTRYPTOPHAN

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:23 , GLN A:47 , THR A:49 , THR A:52 , HOH A:2035 , THR F:25 , ARG F:26 , GLY F:27 , ASP F:29 , THR F:30 , SER F:53BINDING SITE FOR RESIDUE TRP A 81
02AC2SOFTWARESER A:7 , ARG A:26 , THR A:49 , GLU A:50 , HOH A:2014 , SER B:7 , GLN B:47BINDING SITE FOR RESIDUE TRP A 91
03AC3SOFTWARETHR A:25 , ARG A:26 , GLY A:27 , ASP A:29 , THR A:30 , SER A:53 , HOH A:2016 , GLY B:23 , GLN B:47 , THR B:49 , HIS B:51 , THR B:52BINDING SITE FOR RESIDUE TRP B 81
04AC4SOFTWARESER B:7 , ARG B:26 , PHE B:48 , THR B:49 , GLU B:50 , GLN C:47BINDING SITE FOR RESIDUE TRP B 91
05AC5SOFTWARETHR B:25 , ARG B:26 , GLY B:27 , ASP B:29 , THR B:30 , SER B:53 , HOH B:2018 , GLY C:23 , GLN C:47 , THR C:49 , HIS C:51 , THR C:52BINDING SITE FOR RESIDUE TRP C 81
06AC6SOFTWARESER C:7 , ARG C:26 , HOH C:2020 , SER D:7 , GLN D:47BINDING SITE FOR RESIDUE TRP C 91
07AC7SOFTWARETHR C:25 , ARG C:26 , GLY C:27 , ASP C:29 , THR C:30 , SER C:53 , HOH C:2023 , GLY D:23 , GLN D:47 , THR D:49 , THR D:52BINDING SITE FOR RESIDUE TRP D 81
08AC8SOFTWARESER D:7 , ARG D:26 , THR D:49 , GLU D:50 , HOH D:2010 , SER E:7 , GLN E:47BINDING SITE FOR RESIDUE TRP D 91
09AC9SOFTWARETHR D:25 , ARG D:26 , GLY D:27 , ASP D:29 , THR D:30 , SER D:53 , HOH D:2012 , GLY E:23 , GLN E:47 , THR E:49 , HIS E:51 , THR E:52BINDING SITE FOR RESIDUE TRP E 81
10BC1SOFTWARESER E:7 , ARG E:26 , PHE E:48 , THR E:49 , GLU E:50 , HOH E:2016 , SER F:7 , GLN F:47BINDING SITE FOR RESIDUE TRP E 91
11BC2SOFTWARETHR E:25 , ARG E:26 , GLY E:27 , ASP E:29 , THR E:30 , SER E:53 , HOH E:2017 , GLY F:23 , GLN F:47 , THR F:49 , HIS F:51 , THR F:52BINDING SITE FOR RESIDUE TRP F 81
12BC3SOFTWARESER A:7 , GLN A:47 , HOH A:2034 , SER F:7 , ARG F:26 , GLU F:50BINDING SITE FOR RESIDUE TRP F 91

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZZQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZZQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZZQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZZQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZZQ)

(-) 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:65
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:65
                                    16        26        36        46        56        66     
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
               SCOP domains d3zzqa_ A: 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
                  3zzq A  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
                                    16        26        36        46        56        66     


Chain B from PDB  Type:PROTEIN  Length:65
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:65
                                    16        26        36        46        56        66     
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
               SCOP domains d3zzqb_ B: 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
                  3zzq B  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
                                    16        26        36        46        56        66     


Chain C from PDB  Type:PROTEIN  Length:65
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:65
                                    16        26        36        46        56        66     
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
               SCOP domains d3zzqc_ 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
                  3zzq C  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
                                    16        26        36        46        56        66     


Chain D from PDB  Type:PROTEIN  Length:65
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:65
                                    16        26        36        46        56        66     
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
               SCOP domains d3zzqd_ 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
                  3zzq D  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
                                    16        26        36        46        56        66     


Chain E from PDB  Type:PROTEIN  Length:65
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:65
                                    16        26        36        46        56        66     
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
               SCOP domains d3zzqe_ 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
                  3zzq E  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
                                    16        26        36        46        56        66     


Chain F from PDB  Type:PROTEIN  Length:65
 aligned with MTRB_BACSU | P19466 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:65
                                    16        26        36        46        56        66     
            MTRB_BACSU    7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
               SCOP domains d3zzqf_ 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
                  3zzq F  7 SDFVVIKAVEDGVNVIGLTRGTDTKFHHSEKLDKGEVIIAQFTEHTSAIKVRGEALIQTAYGEMK 71
                                    16        26        36        46        56        66
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZZQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZZQ)

(-) 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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  3zzq
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTRB_BACSU | P19466: 1wap 4b27

(-) Related Entries Specified in the PDB File

1wap TRP RNA-BINDING ATTENUATION PROTEIN IN COMPLEX WITH 1WAP 3L-TRYPTOPHAN 1WAP 4
3zzl BACILLUS HALODURANS TRP RNA-BINDING ATTENUATION PROTEIN ( TRAP): A 12-SUBUNIT ASSEMBLY