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(-) Description

Title :  REGULATORY FEATURES OF THE TRP OPERON AND THE CRYSTAL STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN FROM BACILLUS STEAROTHERMOPHILUS.
 
Authors :  X. -P. Chen, A. A. Antson, M. Yang, C. Baumann, E. J. Dodson, G. G. Dodson, P. Gollnick
Date :  31 Mar 99  (Deposition) - 16 Apr 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K
Keywords :  Circular Assembly, 11-Fold Symmetry, Rna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Chen, A. A. Antson, M. Yang, P. Li, C. Baumann, E. J. Dodson, G. G. Dodson, P. Gollnick
Regulatory Features Of The Trp Operon And The Crystal Structure Of The Trp Rna-Binding Attenuation Protein From Bacillus Stearothermophilus.
J. Mol. Biol. V. 289 1003 1999
PubMed-ID: 10369778  |  Reference-DOI: 10.1006/JMBI.1999.2834
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRP RNA-BINDING ATTENUATION PROTEIN
    Chains: A, B, C, D, E, F, G, H, I, J, K
    Engineered: YES
    Expression System Common: PTZSTMTRB IN E. COLI SG62052/PGP1-2
    Expression System Plasmid: PTZSTMTRB
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1234567891011
Asymmetric/Biological Unit : ABCDEFGHIJK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric/Biological Unit (1, 11)
No.NameCountTypeFull Name
1TRP11Ligand/IonTRYPTOPHAN

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:23 , ALA A:46 , GLN A:47 , THR A:49 , HIS A:51 , THR A:52 , HOH A:100 , THR K:25 , ARG K:26 , GLY K:27 , ASP K:29 , THR K:30 , SER K:53 , ALA K:54BINDING SITE FOR RESIDUE TRP K 81
02AC2SOFTWARETHR 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 A 81
03AC3SOFTWARETHR B:25 , ARG B:26 , GLY B:27 , ASP B:29 , THR B:30 , SER B:53 , GLY C:23 , HIS C:34 , ALA C:46 , GLN C:47 , THR C:49 , THR C:52BINDING SITE FOR RESIDUE TRP B 81
04AC4SOFTWARETHR C:25 , ARG C:26 , GLY C:27 , ASP C:29 , THR C:30 , SER C:53 , GLY D:23 , ALA D:46 , GLN D:47 , THR D:49 , THR D:52BINDING SITE FOR RESIDUE TRP C 81
05AC5SOFTWARETHR D:25 , ARG D:26 , GLY D:27 , ASP D:29 , THR D:30 , SER D:53 , GLN E:47 , THR E:49 , THR E:52 , HOH E:83BINDING SITE FOR RESIDUE TRP D 81
06AC6SOFTWARETHR E:25 , ARG E:26 , GLY E:27 , ASP E:29 , THR E:30 , SER E:53 , HOH E:89 , GLN F:47 , THR F:49 , THR F:52BINDING SITE FOR RESIDUE TRP E 81
07AC7SOFTWARETHR F:25 , ARG F:26 , GLY F:27 , ASP F:29 , THR F:30 , SER F:53 , GLN G:47 , THR G:49 , THR G:52 , HOH G:83BINDING SITE FOR RESIDUE TRP G 81
08AC8SOFTWARETHR G:25 , ARG G:26 , GLY G:27 , ASP G:29 , THR G:30 , SER G:53 , HOH G:92 , GLY H:23 , HIS H:34 , ALA H:46 , GLN H:47 , THR H:49 , THR H:52BINDING SITE FOR RESIDUE TRP G 82
09AC9SOFTWARETHR H:25 , ARG H:26 , GLY H:27 , ASP H:29 , THR H:30 , SER H:53 , GLN I:47 , THR I:49 , HIS I:51 , THR I:52 , HOH I:159BINDING SITE FOR RESIDUE TRP H 81
10BC1SOFTWARETHR I:25 , ARG I:26 , GLY I:27 , ASP I:29 , THR I:30 , SER I:53 , GLN J:47 , THR J:49 , HIS J:51 , THR J:52BINDING SITE FOR RESIDUE TRP I 81
11BC2SOFTWARETHR J:25 , ARG J:26 , GLY J:27 , ASP J:29 , THR J:30 , SER J:53 , HOH J:179 , GLY K:23 , GLN K:47 , THR K:49 , THR K:52BINDING SITE FOR RESIDUE TRP J 81

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QAW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QAW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QAW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QAW)

(-) Exons   (0, 0)

(no "Exon" information available for 1QAW)

(-) Sequences/Alignments

Asymmetric/Biological 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 d1qawa_ A: Trp RNA-binding attenuation protein (TRAP)               SCOP domains
               CATH domains 1qawA00 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
                  1qaw 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 d1qawb_ B: Trp RNA-binding attenuation protein (TRAP)                  SCOP domains
               CATH domains 1qawB00 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
                  1qaw 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 d1qawc_ C: Trp RNA-binding attenuation protein (TRAP)                 SCOP domains
               CATH domains 1qawC00 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
                  1qaw 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 d1qawd_ D: Trp RNA-binding attenuation protein (TRAP)                 SCOP domains
               CATH domains 1qawD00 D: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
                  1qaw D  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK 75
                                    16        26        36        46        56        66         


Chain E 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 d1qawe_ E: Trp RNA-binding attenuation protein (TRAP)                 SCOP domains
               CATH domains 1qawE00 E: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
                  1qaw E  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK 75
                                    16        26        36        46        56        66         


Chain F 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 d1qawf_ F: Trp RNA-binding attenuation protein (TRAP)                SCOP domains
               CATH domains 1qawF00 F: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..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1qaw F  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEG 74
                                    16        26        36        46        56        66        


Chain G 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 d1qawg_ G: Trp RNA-binding attenuation protein (TRAP)               SCOP domains
               CATH domains 1qawG00 G: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
                  1qaw G  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 73
                                    16        26        36        46        56        66       


Chain H 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 d1qawh_ H: Trp RNA-binding attenuation protein (TRAP)                SCOP domains
               CATH domains 1qawH00 H: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..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1qaw H  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEG 74
                                    16        26        36        46        56        66        


Chain I 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 d1qawi_ I: Trp RNA-binding attenuation protein (TRAP)               SCOP domains
               CATH domains 1qawI00 I: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..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  1qaw I  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 73
                                    16        26        36        46        56        66       


Chain J 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 d1qawj_ J: Trp RNA-binding attenuation protein (TRAP)               SCOP domains
               CATH domains 1qawJ00 J: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
                  1qaw J  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESE 73
                                    16        26        36        46        56        66       


Chain K 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 d1qawk_ K: Trp RNA-binding attenuation protein (TRAP)                SCOP domains
               CATH domains 1qawK00 K:7-74  [code=2.60.40.50, no name defined]                   CATH domains
           Pfam domains (1) TrpBP-1qawK01 K:7-74                                                 Pfam domains (1)
           Pfam domains (2) TrpBP-1qawK02 K:7-74                                                 Pfam domains (2)
           Pfam domains (3) TrpBP-1qawK03 K:7-74                                                 Pfam domains (3)
           Pfam domains (4) TrpBP-1qawK04 K:7-74                                                 Pfam domains (4)
           Pfam domains (5) TrpBP-1qawK05 K:7-74                                                 Pfam domains (5)
           Pfam domains (6) TrpBP-1qawK06 K:7-74                                                 Pfam domains (6)
           Pfam domains (7) TrpBP-1qawK07 K:7-74                                                 Pfam domains (7)
           Pfam domains (8) TrpBP-1qawK08 K:7-74                                                 Pfam domains (8)
           Pfam domains (9) TrpBP-1qawK09 K:7-74                                                 Pfam domains (9)
          Pfam domains (10) TrpBP-1qawK10 K:7-74                                                 Pfam domains (10)
          Pfam domains (11) TrpBP-1qawK11 K:7-74                                                 Pfam domains (11)
         Sec.struct. author ..eeeeee....eeeeeee......eeeeeee....eeeee....eeeeeee..eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1qaw K  7 SDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEG 74
                                    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, 11)

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

(-) CATH Domains  (1, 11)

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

(-) Pfam Domains  (1, 11)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K   (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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  1qaw
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTRB_GEOSE | Q9X6J6: 1c9s 1gtf 1gtn 1utd 2exs 2ext 2zcz 2zd0 2zp8 2zp9 3aqd 3zzs 4v4f 5eeu 5eev 5eew 5eex 5eey 5eez 5ef0 5ef1 5ef2 5ef3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QAW)