Crystal structure of gated-pore mutant D138H of second DNA-Binding protein under starvation from Mycobacterium smegmatis

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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A histidine aspartate ionic lock gates the iron passage in miniferritins from Mycobacterium smegmatis

Williams, S.M.Chandran, A.V.Vijayabaskar, M.S.Roy, S.Balaram, H.Vishveshwara, S.Vijayan, M.Chatterji, D.

(2014) J Biol Chem 289: 11042-11058

  • DOI: https://doi.org/10.1074/jbc.M113.524421
  • Primary Citation of Related Structures:  
    4M32, 4M33, 4M34, 4M35

  • PubMed Abstract: 

    Dps (DNA-binding protein from starved cells) are dodecameric assemblies belonging to the ferritin family that can bind DNA, carry out ferroxidation, and store iron in their shells. The ferritin-like trimeric pore harbors the channel for the entry and exit of iron. By representing the structure of Dps as a network we have identified a charge-driven interface formed by a histidine aspartate cluster at the pore interface unique to Mycobacterium smegmatis Dps protein, MsDps2. Site-directed mutagenesis was employed to generate mutants to disrupt the charged interactions. Kinetics of iron uptake/release of the wild type and mutants were compared. Crystal structures were solved at a resolution of 1.8-2.2 Å for the various mutants to compare structural alterations vis à vis the wild type protein. The substitutions at the pore interface resulted in alterations in the side chain conformations leading to an overall weakening of the interface network, especially in cases of substitutions that alter the charge at the pore interface. Contrary to earlier findings where conserved aspartate residues were found crucial for iron release, we propose here that in the case of MsDps2, it is the interplay of negative-positive potentials at the pore that enables proper functioning of the protein. In similar studies in ferritins, negative and positive patches near the iron exit pore were found to be important in iron uptake/release kinetics. The unique ionic cluster in MsDps2 makes it a suitable candidate to act as nano-delivery vehicle, as these gated pores can be manipulated to exhibit conformations allowing for slow or fast rates of iron release.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative starvation-induced DNA protecting protein/Ferritin and Dps
A, B, C, D
168Mycolicibacterium smegmatis MC2 155Mutation(s): 1 
Gene Names: DPS2MSMEG_3242MSMEI_3159
Find proteins for A0QXB7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QXB7 
Go to UniProtKB:  A0QXB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QXB7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FE2

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
L [auth C],
M [auth D]
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
P [auth D]
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
N [auth D]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
N [auth D],
O [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.49α = 90
b = 89.49β = 90
c = 420.4γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description