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(-) Description

Title :  TET REPRESSOR CLASS H IN COMPLEX WITH 5A,6-ANHYDROTETRACYCLINE-MG
 
Authors :  L. Schuldt, G. Palm, W. Hinrichs
Date :  03 Mar 08  (Deposition) - 11 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription, Metal-Binding, Antibiotic Resistance, Transcription Regulator, Transcription Regulation Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Aleksandrov, L. Schuldt, W. Hinrichs, T. Simonson
Tet Repressor Induction By Tetracycline: A Molecular Dynamics, Continuum Electrostatics, And Crystallographic Study
J. Mol. Biol. V. 378 896 2008
PubMed-ID: 18395746  |  Reference-DOI: 10.1016/J.JMB.2008.03.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETRACYCLINE RESISTANCE REPRESSOR PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PWH1590
    Expression System Strain: RB791
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PASTEURELLA MULTOCIDA
    Organism Taxid: 747
    Synonym: TETRACYCLINE REPRESSOR CLASS H

 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, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO41Ligand/IonSULFATE ION
3TDC1Ligand/Ion5A,6-ANHYDROTETRACYCLINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
3TDC2Ligand/Ion5A,6-ANHYDROTETRACYCLINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:64 , ASN A:82 , PHE A:86 , HIS A:100 , THR A:103 , ARG A:104 , GLN A:116 , LEU A:134 , ALA A:173 , MG A:1207 , HOH A:2010 , HOH A:2015 , HOH A:2016 , HOH A:2017BINDING SITE FOR RESIDUE TDC A1206
2AC2SOFTWAREHIS A:100 , TDC A:1206 , HOH A:2015 , HOH A:2016 , HOH A:2017BINDING SITE FOR RESIDUE MG A1207
3AC3SOFTWAREGLN A:88 , LEU A:91 , MET A:92BINDING SITE FOR RESIDUE SO4 A1208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.TETR8_PASMD3-63  1A:3-63
2HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR8_PASMD21-52  1A:21-52
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.TETR8_PASMD3-63  2A:3-63
2HTH_TETR_1PS01081 TetR-type HTH domain signature.TETR8_PASMD21-52  2A:21-52

(-) Exons   (0, 0)

(no "Exon" information available for 2VPR)

(-) 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 Q799E2_PASMD | Q799E2 from UniProtKB/TrEMBL  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
         Q799E2_PASMD     2 AKLDKEQVIDNALILLNEVGIEGLTTRKLAQKIGVEQPTLYWHVKNKRALLDALAETILQKHHHHVLPLPNETWQDFLRNNAKSFRQALLMYRDGGKIHAGTRPSESQFETSEQQLQFLCDAGFSLSQAVYALSSIAHFTLGSVLETQEHQESQKEREKVETDTVAYPPLLTQAVAIMDSDNGDAAFLFVLDVMISGLETVLKSAK 207
               SCOP domains d2vpra1 A:2-67 automated matches                                  d2vpra2 A:68-205 automated matches                                                                                                           SCOP domains
               CATH domains 2vprA01 A:2-66 Homeodomain-like                                  2vprA02 A:67-205 Tetracycline Repressor, domain 2                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---------..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vpr A   2 AKLDKEQVIDNALILLNEVGIEGLTTRKLAQKIGVEQPTLYWHVKNKRALLDALAETILQKHHHHVLPLPNETWQDFLRNNAKSFRQALLMYRDGGKIHAGTRPSESQFETSEQQLQFLCDAGFSLSQAVYALSSIAHFTLGSVLETQEHQESQKE---------AYPPLLTQAVAIMDSDNGDAAFLFVLDVMISGLETVLKSAK 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     |   -     | 169       179       189       199      
                                                                                                                                                                                     157       165                                        


Chain A from PDB  Type:PROTEIN  Length:197
 aligned with TETR8_PASMD | P51561 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
          TETR8_PASMD     2 AKLDKEQVIDDALILLNEVGIEGLTTRNVAQKIGVEQPTLYWHVKNKRALLDALAETILQKHHHHVLPLPNETWQDFLRNNAKSFRQALLMYRDGGKIHAGTRPSESQFETSEQQLQFLCDAGFSLSQAVYALSSIAHFTLGSVLETQEHQESQKEREKVETDTVAYPPLLTQAVAIMDSDNGDAAFLFVLDVMISGLETVLKSAK 207
               SCOP domains d2vpra1 A:2-67 automated matches                                  d2vpra2 A:68-205 automated matches                                                                                                           SCOP domains
               CATH domains 2vprA01 A:2-66 Homeodomain-like                                  2vprA02 A:67-205 Tetracycline Repressor, domain 2                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---------..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. 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
                 2vpr A   2 AKLDKEQVIDNALILLNEVGIEGLTTRKLAQKIGVEQPTLYWHVKNKRALLDALAETILQKHHHHVLPLPNETWQDFLRNNAKSFRQALLMYRDGGKIHAGTRPSESQFETSEQQLQFLCDAGFSLSQAVYALSSIAHFTLGSVLETQEHQESQKE---------AYPPLLTQAVAIMDSDNGDAAFLFVLDVMISGLETVLKSAK 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     |   -     | 169       179       189       199      
                                                                                                                                                                                     157       165
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (TETR8_PASMD | P51561)
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.

Chain A   (Q799E2_PASMD | Q799E2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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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