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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX
 
Authors :  P. Orth, D. Schnappinger, W. Hillen, W. Saenger, W. Hinrichs
Date :  25 May 99  (Deposition) - 28 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,M,N
Biol. Unit 1:  A,M,N  (2x)
Keywords :  Transcription Regulation, Repressor/Operator Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Orth, D. Schnappinger, W. Hillen, W. Saenger, W. Hinrichs
Structural Basis Of Gene Regulation By The Tetracycline Inducible Tet Repressor-Operator System.
Nat. Struct. Biol. V. 7 215 2000
PubMed-ID: 10700280  |  Reference-DOI: 10.1038/73324
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3')
    Chains: M
    Engineered: YES
    Other Details: DNA SEQUENCE TAKEN FROM TET OPERATOR CLASS D
    Synonym: TET OPERATOR DNA
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
    Chains: N
    Engineered: YES
    Synonym: TET OPERATOR DNA
    Synthetic: YES
 
Molecule 3 - PROTEIN (TETRACYCLINE REPRESSOR)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K12 DELTA H1 DELTA TRP
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: REGULATORY PROTEIN TETR

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AMN
Biological Unit 1 (2x): AMN

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:100 , LEU A:101 , THR A:103 , ARG A:104 , GLU A:147 , GLU A:150BINDING SITE FOR RESIDUE IMD A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR4_ECOLX21-52  1A:21-52
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR4_ECOLX21-52  2A:21-52

(-) Exons   (0, 0)

(no "Exon" information available for 1QPI)

(-) 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:195
 aligned with TETR4_ECOLX | P0ACT4 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
          TETR4_ECOLX     4 LNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ 206
               SCOP domains d1qpia1 A:4-67 Tetracyclin repressor (Tet-repressor, TetR)      d1qpia2 A:68-206 Tetracyclin repressor (Tet-repressor, TetR)                                                                                SCOP domains
               CATH domains 1qpiA01 A:4-66 Homeodomain-like                                1qpiA02 A:67-205 Tetracycline Repressor, domain 2                                                                                          - CATH domains
               Pfam domains -----TetR_N-1qpiA01 A:9-55                          ------------TetR_C-1qpiA02 A:68-201                                                                                                               ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:21-52        ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qpi A   4 LNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAAL--------ENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ 206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 |       -|      173       183       193       203   
                                                                                                                                                                                 155      164                                          


Chain M from PDB  Type:DNA  Length:15
                                               
                 1qpi M   1 CCTATCAATGATAGA  15
                                    10     


Chain N from PDB  Type:DNA  Length:15
                                               
                 1qpi N   1 TCTATCATTGATAGG  15
                                    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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: TetR_C (33)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (TETR4_ECOLX | P0ACT4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  1qpi
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  TETR4_ECOLX | P0ACT4
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 Related Entries

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

UniProtKB/Swiss-Prot
        TETR4_ECOLX | P0ACT4: 1a6i 1bjz 1ork 2fj1 2ns7 2ns8 2o7o 2tct 2trt 2vke 2vkv 2x6o 2x9d 2xb5 2xgc 2xgd 2xge 2xpu 2xpv 2xpw 2xrl 3fk6 3fk7 3zqf 3zqg 3zqh 3zqi 4abz 4aux 4b1r 4b3a 4d7m 4d7n 4v2f 4v2g 5fkk 5fkl 5fkm 5fkn 5fko

(-) Related Entries Specified in the PDB File

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