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(-) Description

Title :  TETR(D) IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM.
 
Authors :  D. Dalm, J. Proft, G. J. Palm, W. Hinrichs
Date :  30 Aug 10  (Deposition) - 07 Sep 11  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription, Transcription Regulator, Helix-Turn-Helix, Metal Coordination (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Dalm, G. J. Palm, J. Proft, W. Hinrichs
Tetr(D) In Complex With Minocycline.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS D
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPWH 610
    Expression System StrainK-12
    Expression System Taxid83333
    Expression System VariantDELTA H1 DELTA TRP
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2-208
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsC-TERMINUS REMOVED
    SynonymTETRACYCLINE REPRESSOR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
3MIY1Ligand/Ion(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MIY2Ligand/Ion(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:64 , SER A:67 , ASN A:82 , PHE A:86 , HIS A:100 , THR A:103 , ARG A:104 , PRO A:105 , THR A:112 , VAL A:113 , GLN A:116 , LEU A:131 , SER A:138 , LEU A:170 , ALA A:173 , MET A:177 , MG A:1210 , HOH A:2163 , HOH A:2165 , HOH A:2180 , HOH A:2272BINDING SITE FOR RESIDUE MIY A1209
02AC2SOFTWAREHIS A:100 , MIY A:1209 , HOH A:2163 , HOH A:2165 , HOH A:2272BINDING SITE FOR RESIDUE MG A1210
03AC3SOFTWARESER A:2 , ARG A:3 , SER A:74 , SER A:77BINDING SITE FOR RESIDUE CL A1211
04AC4SOFTWARELEU A:4 , GLN A:76 , ARG A:80 , HOH A:2253BINDING SITE FOR RESIDUE CL A1212
05AC5SOFTWARETHR A:26 , THR A:27BINDING SITE FOR RESIDUE CL A1213
06AC6SOFTWAREASN A:5 , ARG A:6 , GLU A:7 , HOH A:2029BINDING SITE FOR RESIDUE CL A1214
07AC7SOFTWARESER A:2 , ASN A:81BINDING SITE FOR RESIDUE CL A1215
08AC8SOFTWARETRP A:75 , GLN A:76BINDING SITE FOR RESIDUE CL A1216
09AC9SOFTWAREARG A:195BINDING SITE FOR RESIDUE CL A1217
10BC1SOFTWARETHR A:26 , ARG A:28 , HOH A:2030 , HOH A:2071BINDING SITE FOR RESIDUE CL A1218

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 2XPV)

(-) 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:199
 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 d2xpva1 A:2-67 Tetracyclin repressor (Tet-repressor, TetR)        d2xpva2 A:68-208 Tetracyclin repressor (Tet-repressor, TetR)                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------...hhhhhhhhhhhh...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
                 2xpv A   2 SRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAAL--------ENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   |     -  |    171       181       191       201       
                                                                                                                                                                                   155      164                                            

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  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  (0, 0)

(no "CATH Domain" information available for 2XPV)

(-) Pfam Domains  (0, 0)

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

(-) 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 2o7o 2tct 2trt 2vke 2vkv 2x6o 2x9d 2xb5 2xgc 2xgd 2xge 2xpu 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

1a6i TET REPRESSOR, CLASS D VARIANT
1bj0 TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
1bjy TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
1bjz TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
1du7 CRYSTAL STRUCTURE OF TET REPRESSOR CLASS D WITH 4- EPI- TETRACYCLINE
1ork TET REPRESSOR, CLASS D IN COMPLEX WITH 9-(N,N- DIMETHYLGLYCYLAMIDO)-6-DEMETHYL-6-DEOXY-TETRACYCLINE
1qpi CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX
2tct
2trt TETRACYCLINE REPRESSOR CLASS D
2vke TET REPRESSOR CLASS D COMPLEXED WITH COBALT AND TETRACYCLINE
2vkv TETR (BD) VARIANT L17G WITH REVERSE PHENOTYPE
2x6o TET REPRESSOR CLASS D IN COMPLEX WITH 7-CHLOR-2- CYANO-ISO-TETRACYCLINE
2x9d TET REPRESSOR (CLASS D) IN COMPLEX WITH ISO-7- CHLORTETRACYCLINE
2xb5 TET REPRESSOR (CLASS D) IN COMPLEX WITH 7- IODOTETRACYCLINE
2xgc CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T -A(I)B OF THE TETRACYCLINE REPRESSOR
2xgd CRYSTAL STRUCTURE OF A DESIGNED HOMODIMERIC VARIANT T- A(L)A(L) OF THE TETRACYCLINE REPRESSOR
2xge CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T -A(A)B OF THE TETRACYCLINE REPRESSOR
2xps TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE AND MAGNESIUM
2xpt TETR(D) IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM.
2xpu TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE.
2xpw TETR(D) IN COMPLEX WITH OXYTETRACYCLINE AND MAGNESIUM.
2xrl TET-REPRESSOR CLASS D T103A WITH DOXYCYCLINE
3zqf STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH ANTIINDUCER PEPTIDE-TAP1
3zqg STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH ANTIINDUCER PEPTIDE-TAP2
3zqh STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE-TIP3
3zqi STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE-TIP2