2IU5 | pdb_00002iu5

Dihydroxyacetone kinase operon activator DhaS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Regulation of the Dha Operon of Lactococcus Lactis: A Deviation from the Rule Followed by the Tetr Family of Transcription Regulators

Christen, S.Srinivas, A.Bahler, P.Zeller, A.Pridmore, D.Bieniossek, C.Baumann, U.Erni, B.

(2006) J Biological Chem 281: 23129

  • DOI: https://doi.org/10.1074/jbc.M603486200
  • Primary Citation Related Structures: 
    2IU4, 2IU5, 2IU6

  • PubMed Abstract: 

    Dihydroxyacetone (Dha) kinases are a novel family of kinases with signaling and metabolic functions. Here we report the x-ray structures of the transcriptional activator DhaS and the coactivator DhaQ and characterize their function. DhaQ is a paralog of the Dha binding Dha kinase subunit; DhaS belongs to the family of TetR repressors although, unlike all known members of this family, it is a transcriptional activator. DhaQ and DhaS form a stable complex that in the presence of Dha activates transcription of the Lactococcus lactis dha operon. Dha covalently binds to DhaQ through a hemiaminal bond with a histidine and thereby induces a conformational change, which is propagated to the surface via a cantilever-like structure. DhaS binding protects an inverted repeat whose sequence is GGACACATN6ATTTGTCC and renders two GC base pairs of the operator DNA hypersensitive to DNase I cleavage. The proximal half-site of the inverted repeat partially overlaps with the predicted -35 consensus sequence of the dha promoter.


  • Organizational Affiliation
    • Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 47.15 kDa 
  • Atom Count: 3,328 
  • Modeled Residue Count: 358 
  • Deposited Residue Count: 390 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HTH-TYPE DHAKLM OPERON TRANSCRIPTIONAL ACTIVATOR DHAS
A, B
195Lactococcus lactis subsp. lactis Il1403Mutation(s): 1 
UniProt
Find proteins for Q9CIV9 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CIV9 
Go to UniProtKB:  Q9CIV9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CIV9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.459α = 90
b = 46.284β = 90
c = 171.939γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Other, Refinement description