1ZLJ | pdb_00001zlj

Crystal Structure of the Mycobacterium tuberculosis Hypoxic Response Regulator DosR C-terminal Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.211 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZLJ

This is version 1.3 of the entry. See complete history

Literature

Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency.

Wisedchaisri, G.Wu, M.Rice, A.E.Roberts, D.M.Sherman, D.R.Hol, W.G.J.

(2005) J Mol Biology 354: 630-641

  • DOI: https://doi.org/10.1016/j.jmb.2005.09.048
  • Primary Citation Related Structures: 
    1ZLJ, 1ZLK

  • PubMed Abstract: 

    On encountering low oxygen conditions, DosR activates the transcription of 47 genes, promoting long-term survival of Mycobacterium tuberculosis in a non-replicating state. Here, we report the crystal structures of the DosR C-terminal domain and its complex with a consensus DNA sequence of the hypoxia-induced gene promoter. The DosR C-terminal domain contains four alpha-helices and forms tetramers consisting of two dimers with non-intersecting dyads. In the DNA-bound structure, each DosR C-terminal domain in a dimer places its DNA-binding helix deep into the major groove, causing two bends in the DNA. DosR makes numerous protein-DNA base contacts using only three amino acid residues per subunit: Lys179, Lys182, and Asn183. The DosR tetramer is unique among response regulators with known structures.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 70.12 kDa 
  • Atom Count: 4,414 
  • Modeled Residue Count: 546 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dormancy Survival Regulator
A, B, C, D, E
A, B, C, D, E, F, G, H
78Mycobacterium tuberculosisMutation(s): 2 
Gene Names: dosRdevRRv3133c
UniProt
Find proteins for P9WMF9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMF9 
Go to UniProtKB:  P9WMF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMF9
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.211 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.069α = 89.9
b = 60.488β = 89.91
c = 74.226γ = 90.99
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary