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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF TETR(D) COMPLEX WITH DOXYCYCLINE
 
Authors :  A. Aleksandrov, J. Proft, W. Hinrichs
Date :  11 Dec 06  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Helix-Turn-Helix, Metal Coordination, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Aleksandrov, J. Proft, W. Hinrichs, T. Simonson
Protonation Patterns In Tetracycline:Tet Repressor Recognition: Simulations And Experiments
Chembiochem V. 8 675 2007
PubMed-ID: 17361981  |  Reference-DOI: 10.1002/CBIC.200600535

(-) Compounds

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS D
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPWH 610
    Expression System StrainK12 DELTA H1 DELTA TRP
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2-208
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DXT1Ligand/Ion(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
3MG1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DXT2Ligand/Ion(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
3MG-1Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:100 , DXT A:222 , HOH A:224 , HOH A:225 , HOH A:226BINDING SITE FOR RESIDUE MG A 223
2AC2SOFTWAREARG A:62 , HIS A:63 , ARG A:92 , TYR A:93BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWARELEU A:4 , GLN A:76 , ARG A:80 , HOH A:394BINDING SITE FOR RESIDUE CL A 302
4AC4SOFTWARESER A:2 , ARG A:3 , SER A:74 , SER A:77BINDING SITE FOR RESIDUE CL A 303
5AC5SOFTWAREHIS A:64 , SER A:67 , ASN A:82 , PHE A:86 , HIS A:100 , ARG A:104 , PRO A:105 , VAL A:113 , GLN A:116 , ILE A:134 , SER A:138 , LEU A:174 , MET A:177 , MG A:223 , HOH A:225 , HOH A:226 , HOH A:321 , HOH A:343BINDING SITE FOR RESIDUE DXT A 222

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O7O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O7O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O7O)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.TETR4_ECOLX3-63  1A:3-63
2HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR4_ECOLX21-52  1A:21-52
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.TETR4_ECOLX3-63  2A:3-63
2HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR4_ECOLX21-52  2A:21-52

(-) Exons   (0, 0)

(no "Exon" information available for 2O7O)

(-) 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:207
 aligned with TETR4_ECOLX | P0ACT4 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
          TETR4_ECOLX     2 ARLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV 208
               SCOP domains d2o7oa1 A:2-67 Tetracyclin repressor (Tet-repressor, TetR)        d2o7oa2 A:68-208 Tetracyclin repressor (Tet-repressor, TetR)                                                                                  SCOP domains
               CATH domains 2o7oA01 A:2-66 Homeodomain-like                                  2o7oA02 A:67-207 Tetracycline Repressor, domain 2                                                                                            - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_TETR_2  PDB: A:3-63 UniProt: 3-63                        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------HTH_TETR_1  PDB: A:21-52        ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o7o A   2 SRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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

(-) CATH Domains  (2, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O7O)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        TETR4_ECOLX | P0ACT41a6i 1bjz 1ork 1qpi 2fj1 2ns7 2ns8 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

2tct THE SAME PROTEIN IN COMPLEX WITH 7-CHLORTETRACYCLINE