3JTH | pdb_00003jth

Crystal structure of a transcriptional regulator HlyU from Vibrio vulnificus CMCP6

• PDB DOI: https://doi.org/10.2210/pdb3JTH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-12 Released: 2010-03-16 
• Deposition Author(s): Nishi, K., Lee, H.J., Park, S.Y., Kim, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.290 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6.

Nishi, K., Lee, H.J., Park, S.Y., Bae, S.J., Lee, S.E., Adams, P.D., Rhee, J.H., Kim, J.S.

(2010) FEBS Lett 

• PubMed: 20178784 
• DOI: https://doi.org/10.1016/j.febslet.2010.02.052
• Primary Citation Related Structures: 
  3JTH


• PubMed Abstract: 
  

  HlyU is a transcription factor of the ArsR/SmtB family and activates the expression of the pathogenic Vibrio vulnificus RTX toxin. In contrast to the other metal-responding ArsR/SmtB proteins, HlyU does not sense metal ions. To provide its structural information, we elucidated the crystal structure of HlyU from V. vulnificus CMCP6 (HlyU_Vv). The monomeric HlyU_Vv architecture of five alpha-helices and two beta-strands, some of which constitute a typical DNA-binding winged helix-turn-helix (wHTH) motif, is very similar to that of other transcription regulators. Nonetheless, the homo-dimeric HlyU_Vv structure shows several different, three-dimensional features in the spatial position and the detailed dimeric interaction, which were not observed in the modeling study based on the same protein family and sequence similarity.

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Organizational Affiliation: 
• Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.9 kDa 
• Atom Count: 1,552 
• Modeled Residue Count: 188 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription activator HlyU	A, B	98	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: VV1_0512

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.290 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.946	α = 90
b = 52.79	β = 103.92
c = 47.862	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Nishi, K., Lee, H.J., Park, S.Y., Kim, J.S.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary