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

(-) Description

Title :  CRYSTAL STRUCTURE OF TETR TRIPLE MUTANT (H64K, S135L, S138I) IN COMPLEX WITH 4-DDMA-ATC
 
Authors :  M. A. Klieber, O. Scholz, S. Lochner, P. Gmeiner, W. Hillen, Y. A. Muller
Date :  16 Dec 08  (Deposition) - 03 Nov 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tetracycline Repressor, Bacterial Transcription Regulation, Altered Inducer Specificity, 4-De-Dimethylamino- Anhydrotetracycline, Antibiotic Resistance, Dna-Binding, Magnesium, Metal-Binding, Repressor, Transcription, Transcription Regulation, Transposable Element (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Klieber, O. Scholz, S. Lochner, P. Gmeiner, W. Hillen, Y. A. Muller
Structural Origins For Selectivity And Specificity In An Engineered Bacterial Repressor-Inducer Pair.
Febs J. V. 276 5610 2009
PubMed-ID: 19712110  |  Reference-DOI: 10.1111/J.1742-4658.2009.07254.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PWH610
    Expression System Strain: RB791
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN (RESIDUES 1-50) AND THE EFFECTOR-BINDING DOMAIN (RESIDUES 51-208)
    Gene: TETR
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: THE FUSION PROTEIN OF DNA-BINDING DOMAIN (RESIDUES 1-50) FROM TETR VARIANT B AND THE EFFECTOR- BINDING DOMAIN (RESIDUES 51-208) FROM TETR VARIANT D
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
14DM2Ligand/Ion(4AS,12AS)-3,10,11,12A-TETRAHYDROXY-6-METHYL-1,12-DIOXO-1,4,4A,5,12,12A-HEXAHYDROTETRACENE-2-CARBOXAMIDE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:100 , 4DM A:210 , GLU B:147BINDING SITE FOR RESIDUE MG A 209
2AC2SOFTWARELYS A:64 , SER A:67 , ASN A:82 , HIS A:100 , THR A:103 , ARG A:104 , PRO A:105 , VAL A:113 , GLN A:116 , ILE A:138 , MG A:209 , HOH A:245 , MET B:177BINDING SITE FOR RESIDUE 4DM A 210
3AC3SOFTWAREHIS B:100 , 4DM B:210 , HOH B:298 , HOH B:302 , HOH B:321BINDING SITE FOR RESIDUE MG B 209
4AC4SOFTWAREMET A:177 , LYS B:64 , SER B:67 , ASN B:82 , HIS B:100 , ARG B:104 , PRO B:105 , GLN B:109 , VAL B:113 , GLN B:116 , LEU B:131 , ILE B:134 , ILE B:138 , MG B:209 , HOH B:212 , HOH B:213 , HOH B:223 , HOH B:262 , HOH B:298 , HOH B:309 , HOH B:317 , HOH B:321BINDING SITE FOR RESIDUE 4DM B 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FK7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FK7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FK7)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FK7)

(-) 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:200
 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 d3fk7a1 A:4-67 Tetracyclin repressor (Tet-repressor, TetR)      d3fk7a2 A:68-206 Tetracyclin repressor (Tet-repressor, TetR)                                                                                SCOP domains
               CATH domains 3fk7A01 A:4-66 Homeodomain-like                                3fk7A02 A:67-206 Tetracycline Repressor, domain 2                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:21-52        ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fk7 A   4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAVEILARHKDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAILAVIHFTLGAVLEQQEHTAALTD---APDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQ 206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153   |   163       173       183       193       203   
                                                                                                                                                                                   157 161                                             


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with TETR4_ECOLX | P0ACT4 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:202
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  
          TETR4_ECOLX     4 LNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALL 205
               SCOP domains d3fk7b1 B:4-67 Tetracyclin repressor (Tet-repressor, TetR)      d3fk7b2 B:68-205 Tetracyclin repressor (Tet-repressor, TetR)                                                                               SCOP domains
               CATH domains 3fk7B01 B:4-66 Homeodomain-like                                3fk7B02 B:67-205 Tetracycline Repressor, domain 2                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-----..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:21-52        --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fk7 B   4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAVEILARHKDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAILAVIHFTLGAVLEQQEHTAALTDRP-----NLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALL 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     |   - |     173       183       193       203  
                                                                                                                                                                                     159   165
   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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FK7)

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    4DM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3fk7)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3fk7
    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
  TETR2_ECOLX | P04483
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TETR4_ECOLX | P0ACT4
    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
  TETR2_ECOLX | P04483
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TETR4_ECOLX | P0ACT4
    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
        TETR2_ECOLX | P04483: 2ns7 2ns8 2vkv 2xgc 2xgd 2xge 3fk6 3zqf 3zqg 3zqh 3zqi 4ac0
        TETR4_ECOLX | P0ACT4: 1a6i 1bjz 1ork 1qpi 2fj1 2ns7 2ns8 2o7o 2tct 2trt 2vke 2vkv 2x6o 2x9d 2xb5 2xgc 2xgd 2xge 2xpu 2xpv 2xpw 2xrl 3fk6 3zqf 3zqg 3zqh 3zqi 4abz 4aux 4b1r 4b3a 4d7m 4d7n 4v2f 4v2g 5fkk 5fkl 5fkm 5fkn 5fko

(-) Related Entries Specified in the PDB File

2o7o 2tct 2vke 2vkv 3fk6