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(-) Description

Title :  CRYSTAL STRUCTURES AND THERMOSTABILITY OF MUTANT TRAP3 A7 (ENGINEERED TRAP)
 
Authors :  M. Watanabe, Y. Mishima, I. Yamashita, S. Y. Park, J. R. H. Tame, J. G. Hed
Date :  15 Nov 07  (Deposition) - 29 Apr 08  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (4x)
Biol. Unit 2:  D,E,F  (4x)
Keywords :  Linker, Artificial, Engineered, Ring Protein, 12-Mer, Rna-Binding, Transcription, Transcription Regulation, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Watanabe, Y. Mishima, I. Yamashita, S. Y. Park, J. R. Tame, J. G. Heddle
Intersubunit Linker Length As A Modifier Of Protein Stability: Crystal Structures And Thermostability Of Mutant Trap.
Protein Sci. V. 17 518 2008
PubMed-ID: 18287284  |  Reference-DOI: 10.1110/PS.073059308

(-) Compounds

Molecule 1 - TRANSCRIPTION ATTENUATION PROTEIN MTRB
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MTRB
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: NCA 26, ATCC 12980
    Synonym: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN, TRP RNA-BINDING ATTENUATION PROTEIN, TRAP

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (4x): ABC   
Biological Unit 2 (4x):    DEF

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
Biological Unit 2 (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 , HOH A:107 , THR C:25 , ARG C:26 , GLY C:27 , ASP C:29 , THR C:30 , SER C:53BINDING SITE FOR RESIDUE TRP A 100
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:52 , HOH B:103BINDING SITE FOR RESIDUE TRP B 100
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 , HIS C:51 , THR C:52 , HOH C:105BINDING SITE FOR RESIDUE TRP C 100
4AC4SOFTWAREGLY D:23 , GLN D:47 , THR D:49 , THR D:52 , HOH D:101 , THR F:25 , ARG F:26 , GLY F:27 , ASP F:29 , THR F:30 , SER F:53BINDING SITE FOR RESIDUE TRP D 100
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:52 , HOH E:102BINDING SITE FOR RESIDUE TRP E 100
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:52 , HOH F:106BINDING SITE FOR RESIDUE TRP F 100

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZCZ)

(-) 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:73
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:73
                                                                                                74   
                                    14        24        34        44        54        64        74   
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK---  -
               SCOP domains d2zcza_ A: Trp RNA-binding attenuation protein (TRAP)                     SCOP domains
               CATH domains 2zczA00 A:7-79  [code=2.60.40.50, no name defined]                        CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeee....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  2zcz A  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKKAAA 79
                                    16        26        36        46        56        66        76   


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

    Alignment length:69
                                    12        22        32        42        52        62         
            MTRB_GEOSE    3 TNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 71
               SCOP domains d2zczb_ B: Trp RNA-binding attenuation protein (TRAP)                 SCOP domains
               CATH domains 2zczB00 B:5-73  [code=2.60.40.50, no name defined]                    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
                  2zcz B  5 TNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 73
                                    14        24        34        44        54        64         


Chain C from PDB  Type:PROTEIN  Length:66
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:66
                                    14        24        34        44        54        64      
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIES 70
               SCOP domains d2zczc_ C: Trp RNA-binding attenuation protein (TRAP)              SCOP domains
               CATH domains 2zczC00 C:7-72  [code=2.60.40.50, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2zcz C  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIES 72
                                    16        26        36        46        56        66      


Chain D from PDB  Type:PROTEIN  Length:73
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:73
                                                                                                74   
                                    14        24        34        44        54        64        74   
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK---  -
               SCOP domains d2zczd_ D: Trp RNA-binding attenuation protein (TRAP)                     SCOP domains
               CATH domains 2zczD00 D:7-79  [code=2.60.40.50, no name defined]                        CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  2zcz D  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKKAAA 79
                                    16        26        36        46        56        66        76   


Chain E from PDB  Type:PROTEIN  Length:68
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:68
                                    14        24        34        44        54        64        
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEG 72
               SCOP domains d2zcze_ E: Trp RNA-binding attenuation protein (TRAP)                SCOP domains
               CATH domains 2zczE00 E:7-74  [code=2.60.40.50, no name defined]                   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
                  2zcz E  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEG 74
                                    16        26        36        46        56        66        


Chain F from PDB  Type:PROTEIN  Length:66
 aligned with MTRB_GEOSE | Q9X6J6 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:66
                                    14        24        34        44        54        64      
            MTRB_GEOSE    5 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIES 70
               SCOP domains d2zczf_ F: Trp RNA-binding attenuation protein (TRAP)              SCOP domains
               CATH domains 2zczF00 F:7-72  [code=2.60.40.50, no name defined]                 CATH domains
           Pfam domains (1) TrpBP-2zczF01 F:7-72                                               Pfam domains (1)
           Pfam domains (2) TrpBP-2zczF02 F:7-72                                               Pfam domains (2)
           Pfam domains (3) TrpBP-2zczF03 F:7-72                                               Pfam domains (3)
           Pfam domains (4) TrpBP-2zczF04 F:7-72                                               Pfam domains (4)
           Pfam domains (5) TrpBP-2zczF05 F:7-72                                               Pfam domains (5)
           Pfam domains (6) TrpBP-2zczF06 F:7-72                                               Pfam domains (6)
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2zcz F  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIES 72
                                    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  (1, 6)

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

(-) Pfam Domains  (1, 6)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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.

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  2zcz
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  MTRB_GEOSE | Q9X6J6
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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 2zd0 2zp8 2zp9 3aqd 3zzs 4v4f 5eeu 5eev 5eew 5eex 5eey 5eez 5ef0 5ef1 5ef2 5ef3

(-) Related Entries Specified in the PDB File

1qaw B. STEAROTHERMOPHILUS WILD-TYPE TRAP
2exs FUSION OF THREE TRAP MONOMERS
2ext FUSION OF FOUR TRAP MONOMERS
2zd0