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(-) Description

Title :  THE STRUCTURE OF DNA-BINDING DOMAIN OF RESPONSE REGULATOR FROM ESCHERICHIA COLI K-12
 
Authors :  D. N. Patil, S. Tomar, P. Kumar
Date :  08 Jun 11  (Deposition) - 21 Mar 12  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription, Response Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Narayanan, L. N. Paul, S. Tomar, D. N. Patil, P. Kumar, D. A. Yernool
Structure-Function Studies Of Dna Binding Domain Of Respons Regulator Kdpe Reveals Equal Affinity Interactions At Dna Half-Sites.
Plos One V. 7 102 2012
PubMed-ID: 22291906  |  Reference-DOI: 10.1371/JOURNAL.PONE.0030102

(-) Compounds

Molecule 1 - KDP OPERON TRANSCRIPTIONAL REGULATORY PROTEIN KDPE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: DNA-BINDING DOMAIN OF KDPE, RESIDUES 124-225
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Variant: MG1655

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ZQ7)

(-) Sites  (0, 0)

(no "Site" information available for 3ZQ7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZQ7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:25 -Gly A:26
2Gly A:26 -Glu A:27
3Ala A:65 -Val A:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZQ7)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPR_PHOBPS51755 OmpR/PhoB-type DNA-binding domain profile.KDPE_ECOLI126-225  1A:6-105

(-) Exons   (0, 0)

(no "Exon" information available for 3ZQ7)

(-) 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:101
 aligned with KDPE_ECOLI | P21866 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:101
                                   134       144       154       164       174       184       194       204       214       224 
           KDPE_ECOLI   125 PDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML 225
               SCOP domains d3zq7a_ A: automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee....eeee..eee..hhhhhhhhhhhhhh...eeehhhhhhhhh......hhhhhhhhhhhhhhhhh........eeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -OMPR_PHOB  PDB: A:6-105 UniProt: 126-225                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3zq7 A   5 PDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML 105
                                    14        24        34        44        54        64        74        84        94       104
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZQ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZQ7)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KDPE_ECOLI | P21866)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000986    bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0001131    transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    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: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.
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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  Cis Peptide Bonds
    Ala A:65 - Val A:66   [ RasMol ]  
    Arg A:25 - Gly A:26   [ RasMol ]  
    Gly A:26 - Glu A:27   [ RasMol ]  
 

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  KDPE_ECOLI | P21866
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDPE_ECOLI | P21866: 1zh2 1zh4 4kfc 4kny 4l85

(-) Related Entries Specified in the PDB File

1zh2 CRYSTAL STRUCTURE OF THE CALCIUM-BOUND RECEIVER DOMAIN OF KDP POTASSIUM TRANSPORT SYSTEM RESPONSE REGULATOR KDPE
1zh4 CRYSTAL STRUCTURE OF THE MG+2/BEF3-BOUND RECEIVER DOMAIN OF KDP POTASSIUM TRANSPORT SYSTEM RESPONSE REGULATOR KDPE