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(-) Description

Title :  TETR(B) IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM
 
Authors :  G. Volkers, W. Hinrichs
Date :  12 Dec 11  (Deposition) - 26 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Volkers, G. J. Palm, W. Hinrichs
Tetr(B) In Complex With Minocycline And Magnesium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN1 0
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymTETRACYCLINE REPRESSOR CLASS B

 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, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MIY1Ligand/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
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MIY2Ligand/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
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:64 , ASN A:82 , PHE A:86 , HIS A:100 , THR A:103 , ARG A:104 , PRO A:105 , GLN A:109 , LEU A:113 , GLN A:116 , LEU A:131 , LEU A:170 , PHE A:177 , MG A:1205 , HOH A:2010 , HOH A:2011 , HOH A:2012BINDING SITE FOR RESIDUE MIY A1204
2AC2SOFTWAREHIS A:100 , MIY A:1204 , HOH A:2010 , HOH A:2011 , HOH A:2012BINDING SITE FOR RESIDUE MG A1205
3AC3SOFTWAREARG A:62 , HIS A:63 , HIS A:93BINDING SITE FOR RESIDUE PO4 A1206
4AC4SOFTWARELYS A:29BINDING SITE FOR RESIDUE PO4 A1207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AC0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AC0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AC0)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.TETR2_ECOLX3-63  1A:3-63
2HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR2_ECOLX21-52  1A:21-52
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.TETR2_ECOLX3-63  2A:3-63
2HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR2_ECOLX21-52  2A:21-52

(-) Exons   (0, 0)

(no "Exon" information available for 4AC0)

(-) 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:197
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:202
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  
          TETR2_ECOLX     2 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKC 203
               SCOP domains d4ac0a1 A:2-67 automated matches                                  d4ac0a2 A:68-203 automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. 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
                 4ac0 A   2 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERE-----SMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKC 203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       | -   |   171       181       191       201  
                                                                                                                                                                                       159   165                                      

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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 4AC0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AC0)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 3zqi

(-) Related Entries Specified in the PDB File

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
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
4abz TETR(D) IN COMPLEX WITH TIGECYCLINE AND MAGNESIUM