3W6V | pdb_00003w6v

Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA

• PDB DOI: https://doi.org/10.2210/pdb3W6V/pdb
• NAKB: 3W6V

• Classification: TRANSCRIPTION ACTIVATOR/DNA
• Organism(s): Streptomyces griseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-22 Released: 2013-09-18 
• Deposition Author(s): Yao, M.D., Ohtsuka, J., Nagata, K., Miyazono, K., Ohnishi, Y., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.278 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Models: experimental

Literature

Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity

Yao, M.D., Ohtsuka, J., Nagata, K., Miyazono, K., Zhi, Y., Ohnishi, Y., Tanokura, M.

(2013) J Biological Chem 288: 31019-31029

• PubMed: 24019524 
• DOI: https://doi.org/10.1074/jbc.M113.473611
• Primary Citation Related Structures: 
  3W6V


• PubMed Abstract: 
  

  AdpA serves as the global transcription factor in the A-factor regulatory cascade, controlling the secondary metabolism and morphological differentiation of the filamentous bacterium Streptomyces griseus. AdpA binds to over 500 operator regions with the consensus sequence 5'-TGGCSNGWWY-3' (where S is G or C, W is A or T, Y is T or C, and N is any nucleotide). However, it is still obscure how AdpA can control hundreds of genes. To elucidate the structural basis of this tolerant DNA recognition by AdpA, we focused on the interaction between the DNA-binding domain of AdpA (AdpA-DBD), which consists of two helix-turn-helix motifs, and a target duplex DNA containing the consensus sequence 5'-TGGCGGGTTC-3'. The crystal structure of the AdpA-DBD-DNA complex and the mutant analysis of AdpA-DBD revealed its unique manner of DNA recognition, whereby only two arginine residues directly recognize the consensus sequence, explaining the strict recognition of G and C at positions 2 and 4, respectively, and the tolerant recognition of other positions of the consensus sequence. AdpA-DBD confers tolerant DNA sequence specificity to AdpA, allowing it to control hundreds of genes as a global transcription factor.

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Organizational Affiliation: 
• From the Departments of Applied Biological Chemistry and.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.54 kDa 
• Atom Count: 1,555 
• Modeled Residue Count: 143 
• Deposited Residue Count: 179 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AdpA	A	147	Streptomyces griseus	Mutation(s): 0  Gene Names: adpA
UniProt
Find proteins for Q9S166 (Streptomyces griseus) Explore Q9S166  Go to UniProtKB:  Q9S166

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3')	B	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*C)-3')	C	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.278 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.51	α = 90
b = 100.64	β = 90
c = 100.91	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
XDS	data scaling
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Yao, M.D., Ohtsuka, J., Nagata, K., Miyazono, K., Ohnishi, Y., Tanokura, M.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description