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(-) Description

Title :  CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION
 
Authors :  Z. Otwinowski, R. W. Schevitz, R. -G. Zhang, C. L. Lawson, A. J. Joachimi R. Marmorstein, B. F. Luisi, P. B. Sigler
Date :  30 Aug 92  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,C,E,G,I,J,K,L
Biol. Unit 1:  A,C,I,J  (1x)
Biol. Unit 2:  E,G,K,L  (1x)
Keywords :  Protein-Dna Complex, Double Helix, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Otwinowski, R. W. Schevitz, R. G. Zhang, C. L. Lawson, A. Joachimiak R. Q. Marmorstein, B. F. Luisi, P. B. Sigler
Crystal Structure Of Trp Repressor/Operator Complex At Atomic Resolution.
Nature V. 335 321 1988
PubMed-ID: 3419502  |  Reference-DOI: 10.1038/335321A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
    Chains: I, J, K, L
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - PROTEIN (TRP REPRESSOR)
    Chains: A, C, E, G
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR.
    Organism Taxid: 316407
    Strain: W3110

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ACEGIJKL
Biological Unit 1 (1x): AC  IJ  
Biological Unit 2 (1x):   EG  KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1TRP4Mod. Amino AcidTRYPTOPHAN
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TRP2Mod. Amino AcidTRYPTOPHAN
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1TRP2Mod. Amino AcidTRYPTOPHAN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:54 , THR A:81 , ARG A:84 , GLY A:85 , SER A:88 , HOH A:125 , ASN C:40 , LEU C:41 , LEU C:43 , DC J:13BINDING SITE FOR RESIDUE TRP A 109
2AC2SOFTWAREASN A:40 , LEU A:41 , LEU A:43 , HOH A:119 , ARG C:54 , THR C:81 , ARG C:84 , GLY C:85 , SER C:88 , DC I:13BINDING SITE FOR RESIDUE TRP A 110
3AC3SOFTWAREARG E:54 , THR E:81 , ARG E:84 , GLY E:85 , SER E:88 , HOH E:112 , ASN G:40 , LEU G:41 , LEU G:43 , DC L:13BINDING SITE FOR RESIDUE TRP E 109
4AC4SOFTWAREASN E:40 , LEU E:41 , LEU E:43 , ARG G:54 , THR G:81 , ARG G:84 , GLY G:85 , SER G:88 , HOH G:116 , DC K:13BINDING SITE FOR RESIDUE TRP G 109

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TRO)

(-) 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:106
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:106
                                                                                                                                 108  
                                    14        24        34        44        54        64        74        84        94       104   |  
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSD--   -
               SCOP domains d1troa_ A: Trp repressor, TrpR                                                                             SCOP domains
               CATH domains 1troA00 A:5-108 Trp Operon Repressor; Chain A                                                           -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1tro A   5 SPYSAAMAEERHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSDWW 110
                                    14        24        34        44        54        64        74        84        94       104   || 
                                                                                                                                 108| 
                                                                                                                                  109 


Chain C from PDB  Type:PROTEIN  Length:99
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:99
                                    19        29        39        49        59        69        79        89        99         
           TRPR_ECOLI    10 AMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSD 108
               SCOP domains d1troc_ C: Trp repressor, TrpR                                                                      SCOP domains
               CATH domains 1troC00 C:10-108 Trp Operon Repressor; Chain A                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1tro C  10 AMAEERHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSD 108
                                    19        29        39        49        59        69        79        89        99         


Chain E from PDB  Type:PROTEIN  Length:98
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:98
                                                                                                                          108 
                                    21        31        41        51        61        71        81        91       101      | 
           TRPR_ECOLI    12 AEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSD-   -
               SCOP domains d1troe_ E: Trp repressor, TrpR                                                                     SCOP domains
               CATH domains 1troE00 E:12-108 Trp Operon Repressor; Chain A                                                   - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1tro E  12 AEERHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSDW 109
                                    21        31        41        51        61        71        81        91       101        


Chain G from PDB  Type:PROTEIN  Length:102
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:102
                                    14        24        34        44        54        64        74        84        94       104  
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLK 106
               SCOP domains d1trog_ G: Trp repressor, TrpR                                                                         SCOP domains
               CATH domains 1troG00 G:5-105 Trp Operon Repressor; Chain A                                                        - CATH domains
           Pfam domains (1) ------------Trp_repressor-1troG01 G:17-104                                                          -- Pfam domains (1)
           Pfam domains (2) ------------Trp_repressor-1troG02 G:17-104                                                          -- Pfam domains (2)
           Pfam domains (3) ------------Trp_repressor-1troG03 G:17-104                                                          -- Pfam domains (3)
           Pfam domains (4) ------------Trp_repressor-1troG04 G:17-104                                                          -- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1tro G   5 SPYSAAMAEERHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLW 109
                                    14        24        34        44        54        64        74        84        94       104||
                                                                                                                              105|
                                                                                                                               109


Chain I from PDB  Type:DNA  Length:19
                                                   
                 1tro I   1 TGTACTAGTTAACTAGTAC  19
                                    10         


Chain J from PDB  Type:DNA  Length:19
                                                   
                 1tro J   1 TGTACTAGTTAACTAGTAC  19
                                    10         


Chain K from PDB  Type:DNA  Length:19
                                                   
                 1tro K   1 TGTACTAGTTAACTAGTAC  19
                                    10         


Chain L from PDB  Type:DNA  Length:19
                                                   
                 1tro L   1 TGTACTAGTTAACTAGTAC  19
                                    10
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (TRPR_ECOLI | P0A881)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  1tro
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPR_ECOLI | P0A881: 1co0 1jhg 1mi7 1rcs 1trr 1wrp 1wrs 1wrt 1zt9 2oz9 3ssw 3ssx 3wrp

(-) Related Entries Specified in the PDB File

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