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(-) Description

Title :  SOLUTION STRUCTURE OF THE DNA COMPLEX OF PHOB DNA-BINDING/TRANSACTIVATION DOMAIN
 
Authors :  T. Yamane, H. Okamura, M. Ikeguchi, Y. Nishimura, A. Kidera
Date :  31 May 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (10x)
Keywords :  Winged Helix-Turn-Helix, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yamane, H. Okamura, M. Ikeguchi, Y. Nishimura, A. Kidera
Water-Mediated Interactions Between Dna And Phob Dna-Binding/Transactivation Domain: Nmr-Restrained Molecular Dynamics In Explicit Water Environment.
Proteins V. 71 1970 2008
PubMed-ID: 18186481  |  Reference-DOI: 10.1002/PROT.21874
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7-CB
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-104
    Gene: PHOB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - 5'- D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'- D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Z33)

(-) Sites  (0, 0)

(no "Site" information available for 2Z33)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z33)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPR_PHOBPS51755 OmpR/PhoB-type DNA-binding domain profile.PHOB_ECOLI129-227  1A:4-102

(-) Exons   (0, 0)

(no "Exon" information available for 2Z33)

(-) Sequences/Alignments

NMR Structure
   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:104
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:104
                                   135       145       155       165       175       185       195       205       215       225    
           PHOB_ECOLI   126 MAVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d2z33a_ A: PhoB                                                                                          SCOP domains
               CATH domains 2z33A00 A:1-104 'winged helix' repressor DNA binding domain                                              CATH domains
               Pfam domains -----------------------Trans_reg_C-2z33A01 A:24-100                                                 ---- Pfam domains
         Sec.struct. author ......eee..eeee....eeee..eee..hhhhhhhhhhhhhh...eeehhhhhhhh........hhhhhhhhhhhhhhhh...hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---OMPR_PHOB  PDB: A:4-102 UniProt: 129-227                                                           -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2z33 A   1 MAVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain B from PDB  Type:DNA  Length:16
                                                
                 2z33 B   1 ACTGTCATAAATCTGT  16
                                    10      


Chain C from PDB  Type:DNA  Length:16
                                                
                 2z33 C   1 ACAGATTTATGACAGT  16
                                    10
   Legend:   → Mismatch (orange background)
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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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (PHOB_ECOLI | P0AFJ5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001108    bacterial-type RNA polymerase holo enzyme binding    Interacting selectively and non-covalently with the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000156    phosphorelay response regulator activity    Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
biological process
    GO:0006817    phosphate ion transport    The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:2000142    regulation of DNA-templated transcription, initiation    Any process that modulates the frequency, rate or extent of DNA-templated transcription initiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2z33
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHOB_ECOLI | P0AFJ5: 1b00 1gxp 1gxq 1qqi 1zes 2iyn 2jb9 2jba 3t72

(-) Related Entries Specified in the PDB File

1qqi THE SAME PROTEIN IN ITS DNA-FREE FORM.