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(-) Description

Title :  THE NATURE OF THE TRAP:ANTI-TRAP COMPLEX
 
Authors :  M. Watanabe, J. G. Heddle, S. Unzai, S. Akashi, S. Y. Park, J. R. H. Tame
Date :  08 Jul 08  (Deposition) - 03 Feb 09  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J  (3x)
Keywords :  Protein-Protein Complex, Transcription, Rna-Binding, Transcription Regulation, Rna Binding Protein-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Watanabe, J. G. Heddle, K. Kikuchi, S. Unzai, S. Akashi, S. Y. Park, J. R. Tame
The Nature Of The Trap-Anti-Trap Complex.
Proc. Natl. Acad. Sci. Usa V. 106 2176 2009
PubMed-ID: 19164760  |  Reference-DOI: 10.1073/PNAS.0801032106

(-) Compounds

Molecule 1 - TRANSCRIPTION ATTENUATION PROTEIN MTRB
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTRB
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN, TRP RNA-BINDING ATTENUATION PROTEIN, TRAP
 
Molecule 2 - TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
    Chains: E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RTPA, YCZA, BSU02530
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: ANTI-TRAP PROTEIN, AT

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (3x): ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1TRP4Ligand/IonTRYPTOPHAN
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1TRP12Ligand/IonTRYPTOPHAN
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS J:12 , CYS J:15 , CYS J:26 , CYS J:29BINDING SITE FOR RESIDUE ZN J 54
02AC2SOFTWARECYS E:12 , LYS E:14 , CYS E:15 , CYS E:26 , ALA E:28 , CYS E:29BINDING SITE FOR RESIDUE ZN E 54
03AC3SOFTWARECYS F:12 , CYS F:15 , CYS F:26 , CYS F:29BINDING SITE FOR RESIDUE ZN F 54
04AC4SOFTWARECYS G:12 , CYS G:15 , CYS G:26 , CYS G:29BINDING SITE FOR RESIDUE ZN G 54
05AC5SOFTWARECYS H:12 , LYS H:14 , CYS H:15 , CYS H:26 , ALA H:28 , CYS H:29BINDING SITE FOR RESIDUE ZN H 54
06AC6SOFTWARECYS I:12 , CYS I:15 , CYS I:26 , CYS I:29BINDING SITE FOR RESIDUE ZN I 54
07AC7SOFTWAREGLY A:23 , GLN A:47 , THR A:49 , HIS A:51 , THR A:52 , THR D:25 , ARG D:26 , GLY D:27 , ASP D:29 , THR D:30 , SER D:53BINDING SITE FOR RESIDUE TRP A 100
08AC8SOFTWARETHR A:25 , GLY A:27 , ASP A:29 , THR A:30 , SER A:53 , GLY B:23 , ALA B:46 , GLN B:47 , THR B:49 , THR B:52 , ILE B:55BINDING SITE FOR RESIDUE TRP B 100
09AC9SOFTWARETHR B:25 , ARG B:26 , GLY B:27 , ASP B:29 , THR B:30 , SER B:53 , GLY C:23 , HIS C:33 , GLN C:47 , THR C:49 , HIS C:51 , THR C:52BINDING SITE FOR RESIDUE TRP C 100
10BC1SOFTWARETHR C:25 , ARG C:26 , GLY C:27 , ASP C:29 , THR C:30 , SER C:53 , GLN D:47 , THR D:49 , HIS D:51 , THR D:52BINDING SITE FOR RESIDUE TRP D 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZP8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZP8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZP8)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZP8)

(-) 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:67
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:67
                                    14        24        34        44        54        64       
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 71
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains 2zp8A00 A:7-73  [code=2.60.40.50, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2zp8 A  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 73
                                    16        26        36        46        56        66       


Chain B from PDB  Type:PROTEIN  Length:70
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:70
                                    14        24        34        44        54        64        74
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK 74
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains 2zp8B00 B:7-76  [code=2.60.40.50, no name defined]                     CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee.eeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  2zp8 B  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK 76
                                    16        26        36        46        56        66        76


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:69
                                    14        24        34        44        54        64         
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK 73
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains 2zp8C00 C:7-75  [code=2.60.40.50, no name defined]                    CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2zp8 C  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK 75
                                    16        26        36        46        56        66         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:69
                                    14        24        34        44        54        64         
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK 73
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains 2zp8D00 D:7-75  [code=2.60.40.50, no name defined]                    CATH domains
           Pfam domains (1) TrpBP-2zp8D01 D:7-75                                                  Pfam domains (1)
           Pfam domains (2) TrpBP-2zp8D02 D:7-75                                                  Pfam domains (2)
           Pfam domains (3) TrpBP-2zp8D03 D:7-75                                                  Pfam domains (3)
           Pfam domains (4) TrpBP-2zp8D04 D:7-75                                                  Pfam domains (4)
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2zp8 D  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK 75
                                    16        26        36        46        56        66         


Chain E from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee........ee..ee........eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2zp8 E  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   


Chain F from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee........ee..ee........eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2zp8 F  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   


Chain G from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee........ee..ee........eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2zp8 G  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   


Chain H from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee........ee..ee........eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2zp8 H  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   


Chain I from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee........ee..ee........eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2zp8 I  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   


Chain J from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee........ee..ee........eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2zp8 J  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50
   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 2ZP8)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: TrpBP] (7)

(-) Gene Ontology  (7, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MTRB_GEOSE | Q9X6J6)
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.

Chain E,F,G,H,I,J   (RTPA_BACSU | O31466)
molecular function
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2zp8
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  RTPA_BACSU | O31466
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTRB_GEOSE | Q9X6J6: 1c9s 1gtf 1gtn 1qaw 1utd 2exs 2ext 2zcz 2zd0 2zp9 3aqd 3zzs 4v4f 5eeu 5eev 5eew 5eex 5eey 5eez 5ef0 5ef1 5ef2 5ef3
        RTPA_BACSU | O31466: 2bx9 2ko8 2zp9

(-) Related Entries Specified in the PDB File

2zp9