Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.06 kDa 
• Atom Count: 2023 
• Residue Count: 230 
• Unique protein chains: 1

5COS

Crystal Structure of the Cytoplasmic Domain of the Pseudomonas putida Anti-sigma Factor PupR

• DOI: 10.2210/pdb5COS/pdb

• Classification: TRANSCRIPTION
• Organism(s): Pseudomonas capeferrum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-20 Released: 2015-09-09 
• Deposition Author(s): Jensen, J.L., Colbert, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.257 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Literature

Mechanistic Implications of the Unique Structural Features and Dimerization of the Cytoplasmic Domain of the Pseudomonas Sigma Regulator, PupR.

Jensen, J.L., Balbo, A., Neau, D.B., Chakravarthy, S., Zhao, H., Sinha, S.C., Colbert, C.L.

(2015) Biochemistry 54: 5867-5877

• PubMed: 26313375 
• DOI: 10.1021/acs.biochem.5b00826
• Primary Citation of Related Structures:  
  5CAM, 5COS


• PubMed Abstract: 
  

Gram-negative bacteria tightly regulate intracellular levels of iron, an essential nutrient. To ensure this strict control, some outer membrane TonB-dependent transporters (TBDTs) that are responsible for iron import stimulate their own transcription in response to extracellular binding by an iron-laden siderophore. This process is mediated by an inner membrane sigma regulator protein (an anti-sigma factor) that transduces an unknown periplasmic signal from the TBDT to release an intracellular sigma factor from the inner membrane, which ultimately upregulates TBDT transcription. Here, we use the Pseudomonas putida ferric-pseudobactin BN7/BN8 sigma regulator, PupR, as a model system to understand the molecular mechanism of this conserved class of sigma regulators. We have determined the X-ray crystal structure of the cytoplasmic anti-sigma domain (ASD) of PupR to 2.0 Å. Size exclusion chromatography, small-angle X-ray scattering, and sedimentation velocity analytical ultracentrifugation all indicate that, in contrast to other ASDs, the PupR-ASD exists as a dimer in solution. Mutagenesis of residues at the dimer interface identified from the crystal structure disrupts dimerization and protein stability, as determined by sedimentation velocity analytical ultracentrifugation and thermal denaturation circular dichroism spectroscopy. These combined results suggest that this type of inner membrane sigma regulator may utilize an unusual mechanism to sequester their cognate sigma factors and prevent transcription activation.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Siderophore-interacting protein	A, B, C, D	86	Pseudomonas capeferrum	Mutation(s): 0  Gene Names: PC358_08100
Find proteins for A0A084CH09 (Pseudomonas capeferrum) Explore A0A084CH09  Go to UniProtKB:  A0A084CH09

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.257 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.459	α = 90
b = 134.621	β = 113.72
c = 34.896	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-07-20 
• Released Date: 2015-09-09 
Deposition Author(s): Jensen, J.L., Colbert, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R15GM113227-01

Revision History 

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence