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(-) Description

Title :  STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE-TIP2
 
Authors :  M. Sevvana, D. Goeke, C. Stoeckle, D. Kaspar, S. Grubmueller, C. Goetz, C. Berens, M. Klotzsche, Y. A. Muller, W. Hillen
Date :  09 Jun 11  (Deposition) - 28 Dec 11  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription, Tetr, Peptidic Effectors, Allostery (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sevvana, C. Goetz, D. Goeke, C. Wimmer, C. Berens, W. Hillen, Y. A. Muller
An Exclusive Alpha/Beta Code Directs Allostery In Tetr-Peptide Complexes.
J. Mol. Biol. V. 416 46 2012
PubMed-ID: 22178479  |  Reference-DOI: 10.1016/J.JMB.2011.12.008

(-) Compounds

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 1-187,188-208
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsCHIMERIC PROTEIN, RESIDUES 1-187 ARE FROM VARIANT B, RESIDUES 188-208 ARE FROM VARIANT D COMPND
 
Molecule 2 - INDUCER PEPTIDE TIP2
    ChainsC, D
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:144 , GLU A:147 , ASP A:148 , PHE A:177 , HOH A:2155 , HOH A:2158 , HIS B:139 , TRP D:12BINDING SITE FOR RESIDUE EDO A 1205
2AC2SOFTWAREHIS A:66 , ASN A:81 , LYS A:84 , HOH A:2225 , GLU B:15 , GLU B:19BINDING SITE FOR RESIDUE EDO A 1206
3AC3SOFTWAREHOH A:2032 , HOH A:2033 , HOH A:2123 , HOH A:2160 , HOH D:2005 , HOH D:2006BINDING SITE FOR RESIDUE MG A 1207
4AC4SOFTWAREASP B:61 , THR B:106 , GLN B:109 , EDO B:1206 , HOH B:2117 , HOH B:2204BINDING SITE FOR RESIDUE EDO B 1205
5AC5SOFTWAREASP B:61 , LYS B:108 , GLN B:109 , EDO B:1205BINDING SITE FOR RESIDUE EDO B 1206
6AC6SOFTWAREARG B:87 , VAL B:145 , ALA B:182 , GLU B:183 , HOH B:2155 , HOH B:2188BINDING SITE FOR RESIDUE EDO B 1207
7AC7SOFTWARESER A:7 , ASN A:11 , GLU A:58 , ASP A:61 , ARG A:62 , SER B:7 , ILE B:10 , ASN B:11 , GLU B:58 , ASP B:61 , ARG B:62 , HOH B:2062 , HOH B:2205 , HOH B:2206 , HOH B:2207BINDING SITE FOR RESIDUE PG4 B 1208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR2_ECOLX21-52
 
  2A:21-52
B:21-52

(-) Exons   (0, 0)

(no "Exon" information available for 3ZQI)

(-) 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:201
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:201
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
          TETR2_ECOLX     4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCE 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: A:21-52        -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqi A   4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFSPLEGESWQDFLRNNAKSFRNALLSHRDGAKVHLGTRPTEKQYETLENQLAFLTQQGFSLENALYALSAVGHFTLGSVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLHGLESLIRGFEVQLTAL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:201
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
          TETR2_ECOLX     4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCE 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------HTH_TETR_1  PDB: B:21-52        -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqi B   4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFSPLEGESWQDFLRNNAKSFRNALLSHRDGAKVHLGTRPTEKQYETLENQLAFLTQQGFSLENALYALSAVGHFTLGSVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLHGLESLIRGFEVQLTAL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 

Chain C from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 3zqi C   3 SVLAARARMWMWHW  16
                                    12    

Chain D from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 3zqi D   3 SVLAARARMWMWHW  16
                                    12    

   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  (0, 0)

(no "SCOP Domain" information available for 3ZQI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TETR2_ECOLX | P04483)
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
        TETR2_ECOLX | P044832ns7 2ns8 2vkv 2xgc 2xgd 2xge 3fk6 3fk7 3zqf 3zqg 3zqh 4ac0
        TETR4_ECOLX | P0ACT41a6i 1bjz 1ork 1qpi 2fj1 2ns7 2ns8 2o7o 2tct 2trt 2vke 2vkv 2x6o 2x9d 2xb5 2xgc 2xgd 2xge 2xpu 2xpv 2xpw 2xrl 3fk6 3fk7 3zqf 3zqg 3zqh 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 THE COMPLEX FORMED BETWEEN TET REPRESSOR AND TETRACYCLINE- MG2+ REVEALS MECHANISM OF ANTIBIOTIC RESISTANCE
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.
2xpv TETR(D) IN COMPLEX WITH MINOCYCLINE AND MG.
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