Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 61.29 kDa 
• Atom Count: 4263 
• Residue Count: 556 
• Unique protein chains: 1

4IVN

The Vibrio vulnificus NanR protein complexed with ManNAc-6P

• DOI: 10.2210/pdb4IVN/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Vibrio vulnificus YJ016
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-23 Released: 2013-07-17 
• Deposition Author(s): Hwang, J., Kim, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structural insights into the regulation of sialic acid catabolism by the Vibrio vulnificus transcriptional repressor NanR

Hwang, J., Kim, B.S., Jang, S.Y., Lim, J.G., You, D.J., Jung, H.S., Oh, T.K., Lee, J.O., Choi, S.H., Kim, M.H.

(2013) Proc Natl Acad Sci U S A 110: E2829-E2837

• PubMed: 23832782 
• DOI: 10.1073/pnas.1302859110
• Primary Citation of Related Structures:  
  4IVN


• PubMed Abstract: 
  

Pathogenic and commensal bacteria that experience limited nutrient availability in their host have evolved sophisticated systems to catabolize the mucin sugar N-acetylneuraminic acid, thereby facilitating their survival and colonization. The correct function of the associated catabolic machinery is particularly crucial for the pathogenesis of enteropathogenic bacteria during infection, although the molecular mechanisms involved with the regulation of the catabolic machinery are unknown. This study reports the complex structure of NanR, a repressor of the N-acetylneuraminate (nan) genes responsible for N-acetylneuraminic acid catabolism, and its regulatory ligand, N-acetylmannosamine 6-phosphate (ManNAc-6P), in the human pathogenic bacterium Vibrio vulnificus. Structural studies combined with electron microscopic, biochemical, and in vivo analysis demonstrated that NanR forms a dimer in which the two monomers create an arched tunnel-like DNA-binding space, which contains positively charged residues that interact with the nan promoter. The interaction between the NanR dimer and DNA is alleviated by the ManNAc-6P-mediated relocation of residues in the ligand-binding domain of NanR, which subsequently relieves the repressive effect of NanR and induces the transcription of the nan genes. Survival studies in which mice were challenged with a ManNAc-6P-binding-defective mutant strain of V. vulnificus demonstrated that this relocation of NanR residues is critical for V. vulnificus pathogenesis. In summary, this study presents a model of the mechanism that regulates sialic acid catabolism via NanR in V. vulnificus.

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Organizational Affiliation: 

Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B	278	Vibrio vulnificus YJ016	Mutation(s): 0  Gene Names: VVA1198
Find proteins for Q7MD38 (Vibrio vulnificus (strain YJ016)) Explore Q7MD38  Go to UniProtKB:  Q7MD38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMX	A, B	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose C8 H16 N O9 P BRGMHAYQAZFZDJ-UOLFYFMNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.205	α = 90
b = 109.205	β = 90
c = 82.472	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-23 
• Released Date: 2013-07-17 
Deposition Author(s): Hwang, J., Kim, M.H.

Revision History 

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary