5YEJ

Crystal structure of BioQ with its naturel double-stranded DNA operator

• PDB DOI: https://doi.org/10.2210/pdb5YEJ/pdb
• NAKB: 5YEJ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mycolicibacterium smegmatis MC2 155, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-17 Released: 2018-09-26 
• Deposition Author(s): Yan, L., Guan, Z.Y., Zou, T.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Structural insights into operator recognition by BioQ in the Mycobacterium smegmatis biotin synthesis pathway.

Yan, L., Tang, Q., Guan, Z., Pei, K., Zou, T., He, J.

(2018) Biochim Biophys Acta Gen Subj 1862: 1843-1851

• PubMed: 29852200 
• DOI: https://doi.org/10.1016/j.bbagen.2018.05.015
• Primary Citation of Related Structures:  
  5YEJ, 5YEK


• PubMed Abstract: 
  

  Biotin is an essential cofactor in living organisms. The TetR family transcriptional regulator (TFTR) BioQ is the main regulator of biotin synthesis in Mycobacterium smegmatis. BioQ represses the expression of its target genes by binding to a conserved palindromic DNA sequence (the BioQ operator). However, the mechanism by which BioQ recognizes this DNA element has not yet been fully elucidated.

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Organizational Affiliation: 

College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92.95 kDa 
• Atom Count: 5,011 
• Modelled Residue Count: 560 
• Deposited Residue Count: 753 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator	A, B, F [auth C]	232	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEI_3111
UniProt
Find proteins for A0QX69 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QX69  Go to UniProtKB:  A0QX69

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3')	C [auth D], E [auth G]	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3')	D [auth F]	19	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.687	α = 90
b = 212.468	β = 99.43
c = 88.126	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Yan, L., Guan, Z.Y., Zou, T.T.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Database references
• Version 1.2: 2018-10-10
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references, Structure summary