Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 16.98 kDa 
• Atom Count: 1185 
• Modelled Residue Count: 149 
• Deposited Residue Count: 149 
• Unique protein chains: 1

5H46

Mycobacterium smegmatis Dps1 mutant - F47E

• PDB DOI: 10.2210/pdb5H46/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-10-31 Released: 2017-09-06 
• Deposition Author(s): Williams, S.M., Chandran, A.V., Vijayan, M., Chatterji, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.260 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

A Mutation Directs the Structural Switch of DNA Binding Proteins under Starvation to a Ferritin-like Protein Cage.

Williams, S.M., Chandran, A.V., Prakash, S., Vijayan, M., Chatterji, D.

(2017) Structure 25: 1449-1454.e3

• PubMed: 28823472 
• DOI: 10.1016/j.str.2017.07.006
• Primary Citation of Related Structures:  
  5H46


• PubMed Abstract: 
  

Proteins of the ferritin family are ubiquitous in living organisms. With their spherical cage-like structures they are the iron storehouses in cells. Subfamilies of ferritins include 24-meric ferritins and bacterioferritins (maxiferritins), and 12-meric Dps (miniferritins). Dps safeguards DNA by direct binding, affording physical protection and safeguards from free radical-mediated damage by sequestering iron in its core. The maxiferritins can oxidize and store iron but cannot bind DNA. Here we show that a mutation at a critical interface in Dps alters its assembly from the canonical 12-mer to a ferritin-like 24-mer under crystallization. This structural switch was attributed to the conformational alteration of a highly conserved helical loop and rearrangement of the C-terminus. Our results demonstrate a novel concept of mutational switch between related protein subfamilies and corroborate the popular model for evolution by which subtle substitutions in an amino acid sequence lead to diversification among proteins.

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Related Citations: 

• Molecular mechanism of in vitro oligomerization of Dps from Mycobacterium smegmatis: mutations of the residues identified by "interface cluster" analysis.
  Chowdhury, R.P., Vijayabaskar, M.S., Vishveshwara, S., Chatterji, D.
  (2008) Biochemistry 47: 11110

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA protection during starvation protein	A	149	Mycolicibacterium smegmatis MC2 155	Mutation(s): 1  Gene Names: dps, MSMEG_6467, MSMEI_6295 EC: 1.16
UniProt
Find proteins for A0R692 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R692  Go to UniProtKB:  A0R692

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	B [auth A], C [auth A], D [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.260 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.07	α = 90
b = 175.07	β = 90
c = 175.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	data reduction
REFMAC	data scaling
Coot	model building
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-31 
• Released Date: 2017-09-06 
Deposition Author(s): Williams, S.M., Chandran, A.V., Vijayan, M., Chatterji, D.

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Funding Organization	Location	Grant Number
	India	--

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references