1ZLK | pdb_00001zlk

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

• PDB DOI: https://doi.org/10.2210/pdb1ZLK/pdb
• NAKB: 1ZLK

• Classification: Transcription/DNA
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-06 Released: 2006-01-31 
• Deposition Author(s): Wisedchaisri, G., Wu, M., Rice, A.E., Roberts, D.M., Sherman, D.R., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.288 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Model: experimental

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

• PubMed: 16246368 
• 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.51 kDa 
• Atom Count: 2,018 
• Modeled Residue Count: 179 
• Deposited Residue Count: 276 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dormancy Survival Regulator	C [auth A], D [auth B]	95	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: dosR, devR, Rv3133c
UniProt
Find proteins for P9WMF9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMF9  Go to UniProtKB:  P9WMF9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*CP*CP*CP*GP*CP*GP*CP*TP*TP*TP*GP*GP*GP*GP*AP*CP*TP*AP*AP*AP*GP*TP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*GP*GP*CP*CP*AP*CP*GP*AP*T)-3'	A [auth C]	43	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*TP*GP*GP*CP*CP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*AP*CP*TP*TP*TP*AP*GP*TP*CP*CP*CP*CP*AP*AP*AP*GP*CP*GP*CP*GP*GP*GP*CP*CP*AP*T)-3'	B [auth D]	43	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.288 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.397	α = 90
b = 58.791	β = 125.5
c = 82.933	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-31 
Deposition Author(s): Wisedchaisri, G., Wu, M., Rice, A.E., Roberts, D.M., Sherman, D.R., Hol, W.G.J.

Revision History  

• 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: 2023-08-23
  Changes: Data collection, Database references, Refinement description