Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL ACTIVATION OF THE TRANSCRIPTIONAL REPRESSOR ETHR FROM M. TUBERCULOSIS BY SINGLE AMINO-ACID CHANGE MIMICKING NATURAL AND SYNTHETIC LIGANDS
 
Authors :  X. Carette, N. Blondiaux, E. Willery, S. Hoos, N. Lecat-Guillet, Z. Len A. Wohlkonig, R. Wintjens, S. Soror, F. Fr Nois, B. Diri, V. Villeret, P. England, G. Lippens, B. Deprez, C. Locht, N. Willand, A. Baulard
Date :  07 Sep 11  (Deposition) - 21 Dec 11  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tetr-Family, Transcritptional Regulatory Repressor, Dna Binding Protein, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Carette, N. Blondiaux, E. Willery, S. Hoos, N. Lecat-Guillet, Z. Lens, A. Wohlkonig, R. Wintjens, S. H. Soror, F. Frenois, B. Dirie, V. Villeret, P. England, G. Lippens, B. Deprez, C. Locht, N. Willand, A. R. Baulard
Structural Activation Of The Transcriptional Repressor Ethr From Mycobacterium Tuberculosis By Single Amino Acid Change Mimicking Natural And Synthetic Ligands.
Nucleic Acids Res. V. 40 3018 2011
PubMed-ID: 22156370  |  Reference-DOI: 10.1093/NAR/GKR1113

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR ETHR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ETHR, ETAR, MT3970, RV3855
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FO51Ligand/Ion3-OXO-3-{4-[3-(THIOPHEN-2-YL)-1,2,4-OXADIAZOL-5-YL]PIPERIDIN-1-YL}PROPANENITRILE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FO52Ligand/Ion3-OXO-3-{4-[3-(THIOPHEN-2-YL)-1,2,4-OXADIAZOL-5-YL]PIPERIDIN-1-YL}PROPANENITRILE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:102 , GLY A:106 , ILE A:107 , PHE A:110 , TYR A:148 , THR A:149 , ASN A:176 , ASN A:179 , TRP A:207BINDING SITE FOR RESIDUE FO5 A 217

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TP0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:191 -Pro A:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TP0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TP0)

(-) Exons   (0, 0)

(no "Exon" information available for 3TP0)

(-) 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:188
 aligned with ETHR_MYCTO | P9WMC0 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:191
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
           ETHR_MYCTO    24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAENPADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
               SCOP domains d3tp0a1 A:24-93 Ethr repressor                                        ---d3tp0a2 A:97-214 Ethr repressor                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tp0 A  24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAEN---TDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
                                    33        43        53        63        73        83        93   |   103       113       123       133       143       153       163       173       183       193       203       213 
                                                                                                93  97                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:188
 aligned with ETHR_MYCTU | P9WMC1 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:191
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
           ETHR_MYCTU    24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAENPADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
               SCOP domains d3tp0a1 A:24-93 Ethr repressor                                        ---d3tp0a2 A:97-214 Ethr repressor                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tp0 A  24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAEN---TDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
                                    33        43        53        63        73        83        93   |   103       113       123       133       143       153       163       173       183       193       203       213 
                                                                                                93  97
   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  (0, 0)

(no "CATH Domain" information available for 3TP0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TP0)

(-) Gene Ontology  (7, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (ETHR_MYCTO | P9WMC0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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.

Chain A   (ETHR_MYCTU | P9WMC1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FO5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:191 - Pro A:192   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3tp0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ETHR_MYCTO | P9WMC0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ETHR_MYCTU | P9WMC1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ETHR_MYCTO | P9WMC0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ETHR_MYCTU | P9WMC1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ETHR_MYCTO | P9WMC0: 1t56 1u9n 1u9o 3g1l 3g1m 3g1o 3o8g 3o8h 3q0u 3q0v 3q0w 3q3s 3qpl 3sdg 3sfi 3tp3 4dw6 4m3b 4m3d 4m3e 4m3f 4m3g 5ezg 5ezh 5f04 5f08 5f0c 5f0f 5f0h 5f1j 5f27 5j3l
        ETHR_MYCTU | P9WMC1: 1t56 1u9n 1u9o 3g1l 3g1m 3g1o 3o8g 3o8h 3q0u 3q0v 3q0w 3q3s 3qpl 3sdg 3sfi 3tp3 4dw6 4m3b 4m3d 4m3e 4m3f 4m3g 5eyr 5ezg 5ezh 5f04 5f08 5f0c 5f0f 5f0h 5f1j 5f27 5j1r 5j1u 5j1y 5j3l 5mwo 5mxk

(-) Related Entries Specified in the PDB File

3tp3